Overview comment

This manuscript provides the similarities and/or differences of responses due to the choice of chemical mechanism and emission inventories. I will agree with the final remark, “the evaluation of the control strategies may require an ensemble approach with multiple inventories and mechanisms,” for a better understanding of the model and clear guidance for policymakers. I could follow most parts of this manuscript; however, I am afraid that the manuscript may be hard to understand for those outside of modeling researcher. The fundamental revision, especially in the introduction and methodology, will be required. Please address the following comments.

Major comments

• Explanation of SAPRC mechanism: Lines 79-81, and even reading after Line 127-144 (Section 2.1), it was very hard to understand the SAPRC mechanism, especially for an unfamiliar researcher in modeling. Please rewrite and reorganize these parts to provide a clear introduction and explanation of the method.
• Configuration of experiments: Due to the inconsistency of the targeted year of the emission inventory, a large difference in the comparison is natural. What is the motivation for using different years? Because of this inconsistency of the year in the emission inventory and observation, how do we understand the result of the modeling evaluation (Section 3.1)? Unfortunately, without understanding this modeling comparison design, I cannot go on to read after Section 3.2.

Specific comments

• Line 100 and Lines 147-149: My simple question is why EDGAR was not used in this study. Please clarify the reason for the selection of MEIC and REAS in this study. From the website indicated in Line 148, REAS seems to be updated to 3.2.1. Why was the older version applied even though the release of the updated version?
• Line 161: The reason why July was analyzed in this study was unclear. Please clearly introduce this reason.
• Line 167: Why was S18-MEIC not conducted?
• Lines 172-195: Again, I wonder what the intention is of this discussion under the configuration of a different year’s emission inventory.
• Line 223: It is better to explicitly state “20, 40, 50, 60, and 80%”.
• Lines 251-253 (Figure 1): I understand that the emission outside China is unified by REAS. So, what stands for a larger difference over Mongolia, eastern Russia, Japan, and eastern India shown in Fig. 1(c)? Is this due to the different treatment in S11 and S18? Anyway, a detailed introduction to understand the differences in the SAPRC scheme is insufficient, and we do not follow these differences.
• Figures 3 and 4: The above comment could also be repeated for radicals of OH and NO3. A larger difference outside China was obvious in Fig. 3(c) and Fig. 4(c). However, there is no mention of these differences in Section 3.3. Please clarify.
• Figure 5: Same in Fig. 5(c).

Technical corrections

• Line 152: No need to spell out SAPRC.
• Lines 169-171: This sentence is redundant in Lines 155-156.
• Line 252 (and some parts in this manuscript): “summer” should be “July”.

This study investigated the uncertainties of emission controls on atmospheric oxidation and air pollutant concentrations by comparing different chemical mechanisms and inventories using an advanced CMAQ model. The manuscript is well-organized, clearly written, and the conclusions are well-supported by the presented data. These findings are timely and provide valuable insights for designing effective region-specific emission control strategies. I recommend this manuscript for publication in ACP after addressing the following minor revisions.

Minor suggestions:

1. Line 28: Since the full name of SIA has already been introduced, the abbreviation can be used directly here.
2. Lines 181-183: The statement “Note that OLE and TRP1 emissions are for the S11 mechanisms” is somewhat unclear. The authors should rephrase this sentence to improve clarity.
3. Lines 241-243: The criteria suggested by the US EPA are better to be stated in the text for clarity.
4. Lines 246-247: The current justification appears weak. The authors should revise this sentence.
5. Lines 257-258: The authors attribute high O3 levels over water bodies to lower O3 dry deposition velocities over the ocean. Is there existing literature supporting this argument? A reference is need here.
6. Line 274: The full term for SIA should be provided upon its first appearance in the main text. In addition, Figure 7 should explicitly list the SIA components for clarity.
7. Lines 494 and 497: Since O3-8h and SIA have been previously defined, the abbreviation can be used directly without reintroducing the full terms.