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Understanding crop potential yields, yield gaps, and optimal agronomic management practices helps in identifying the limiting factors, scope, and ways to achieve sustainable intensified agricultural production. Here, using detailed field trial data collected from 1981 to 2009 at 11 agro-meteorological experimental stations and the crop model CERES-Rice, we investigated changes in potential yields, water- and nitrogen-stressed yields, and yield gaps of rice in the major rice cultivation regions of China during the collection period. We further identified the optimal nitrogen application rate, transplanting date, and cultivar traits for the sustainable intensification of rice production systems in different regions. Owing to climate change, the potential rice yields declined or changed little in the Middle and Lower Reaches of the Yangtze River (MLRYR), while they increased or changed little in the Northeastern China Plain (NECP) during 1981-2009. Rice yield gaps shrank in the major rice production regions because the actual yields increased and approached the potential yields. The average yield gap was 16.0% in the 2000s, with water and nitrogen stresses being the limiting factors in the NECP and water stress being the major limiting factor in the MLRYR. The nitrogen application rate was suggested to be increased by 47.5% and 21.7% for single rice (i.e., rice cultivated in a single season per year) in the NECP and MLRYR, respectively, and increased by 5.2% for early rice (i.e., rice cultivated in the early season in a rice-rice rotation system per year). However, it was suggested to be reduced by 13.1% for late rice (i.e., rice cultivated in the late season in a rice-rice rotation system per year). Early transplanting could increase the yield, while late transplanting could decrease the yield. The impacts were greater for single rice in the NECP and late rice in the MLRYR than for single rice and early rice in the MLRYR. Cultivars with longer growth durations, and greater spikelet numbers and grain weights, could significantly increase the rice yield by 14.8%-45.6%. The optimal cultivars, combined with advancing transplanting by 10 d, could increase rice yields by 29.2%-68.9%. Our findings provide new approaches, important insights, and effective options for the sustainable intensification of rice production systems in different regions of China.