Abstract: This study explored the impacts of different management measures on the annual emissions of methane (CH₄) and nitrous oxide (N₂O) from the main rice-based cropping systems in Hubei Province using the denitrification-decomposition (DNDC) model and observed emission data to estimate the annual greenhouse gas emissions via a geographic information system (ArcGIS). In 2019, rice–wheat (RW) and rice–ratoon rice (RO) cropping systems were implemented in Zaoyang City of Northwest Hubei, RO and rice–oilseed rape (RR) cropping systems were implemented in Wuxue City of Southeast Hubei, and RW, RO, and RR cropping systems were implemented in Qianjiang City of the Jianghan Plain. There were two cultivation modes for each rice-based system: conventional cultivation and optimized cultivation. The optimized mode included deep application of nitrogen fertilizer, water-saving irrigation, and straw returning to the field. The annual fluxes of CH₄ and N₂O were measured using the static closed chamber method. The field validation results showed that the normalized root mean square error between the observed and simulated values of CH₄ and N₂O emissions ranged from 19.3% to 24.2% under different rice-based cropping systems with different management practices, and the degree of model fitting was acceptable. According to the simulation results of the DNDC model, the global warming potential (GWP) for the rice growing regions in Hubei Province followed the order of Jianghan Plain > Southeast Hubei > Northwest Hubei, and the annual cumulative emissions of CH₄, N₂O, and GWP under different rice-based cropping systems in different regions was in the order of RW > RO > RR. The cultivation modes significantly affected the CH₄ and N₂O emissions. Compared with conventional cultivation, optimized cultivation lowered the CH₄ emissions per unit area by 9.5%–18.0%, 7.3%–18.4%, and 18.2%–22.4% under RW, RO, and RR, respectively. The N₂O emissions lowered by 4.2%–14.2%, 6.9%–24.7%, and 8.8%–18.1%, respectively. Moreover, compared with conventional cultivation, optimized cultivation decreased the annual cumulative CH₄ emissions by 11.8%, 14.4%, and 16.3% in Northwest Hubei, Southeast Hubei, and the Jianghan Plain, respectively, and decreased the annual cumulative N₂O emissions by 82.4%, 77.5%, and 83.0%, respectively. Under optimized cultivation, the GWP for Northwest Hubei was in the order of Xiangyang > Shiyan > Shennongjia, that for Southeast Hubei was in the order Huanggang > Xianning > Wuhan > Huangshi > Ezhou, and that for the Jianghan Plain was in the order Jingzhou > Jingmen > Xiaogan > Suizhou > Tianmen > Xiantao > Qianjiang. Our results show that the DNDC model can suitably simulate the greenhouse gas emissions of different rice-based cropping systems in Hubei Province. An optimized cultivation mode is needed to mitigate greenhouse gas emissions during rice production in Hubei Province.