General Comments

Simulating the complex relationships between water, crop yield, and greenhouse gases at a region scale based on process-based model is a challenge. To address this problem, this study proposes a novel framework that simulates regional rice yield, water use, and greenhouse gas emissions in response to various irrigation schemes. This framework integrates critical physiological processes, upscales model parameters, and employs multi-objective optimization. It has been carefully evaluated. Overall, the manuscript is well-structured and well-written. With a few enhancements, I believe this study would make a significant contribution to Geoscientific Model Development.

1. The authors showed large spatial variabilities in regulation potentials while less explanations are provided. Understanding the driving factors behind these variations is essential for designing more targeted and effective irrigation schemes. A more detailed analysis of the spatial patterns and their underlying drivers would greatly benefit the readers' comprehension and application of the findings.
2. Experimental observations are important for improving and calibrating the WHCNS model in this study. The authors also discussed uncertainties associated with observation availability. However, the current description lacks clarity regarding the geographical distribution and environmental context of these observations (Lines 198-228). Detailed information on the observation sites, including their locations and conditions, is crucial for identifying areas for further research and for situating the study's findings within a broader geographical context.

Specific Comments

1. Line 126, please provide full name of NSGA-II and related references.
2. Line 168-194, the model running requires a lot of input data for both site and regional simulations, including variables related to climate, soil and management practices. Although the authors have already provided such information in the Method section, a separate summary table are helpful for clearer view.
3. Line 177, delete the spacing after the reference and please carefully check other formatting errors.
4. Line 208-210, why only observations at the soil depth of 15-20 cm were included?
5. Line 590, please provide full name and related references of the DNDC and DLEM model.
6. Line 701-704, only national results of the tradeoffs or synergies relationships between different variables were stated. Please discuss more about their spatial heterogeneity.

This study improves process-based modeling of the complex food-water-climate nexus under various water management schemes by incorporating the effects of three critical physiological stages and upscaling model parameters. It provides a practical tool for multi-objective optimization of water management, delivering co-benefits such as ensuring food production, conserving water, and reducing greenhouse gas emissions in rice fields.

In my opinion, the manuscript aligns well with the scope of the journal and contributes to the advancement of process-based modeling. The manuscript is well-structured and presents a comprehensive analysis. The selection of methods is well-supported by theoretical foundations, and all model parameters and assumptions are appropriately validated, ensuring the reliability of the results. The figures are accurate and effectively illustrate the findings. Additionally, the study's limitations have been thoroughly discussed. While the methods used are not entirely novel, they are effective and appropriate.

Therefore, I recommend acceptance without revision.