This study aimed to compare different “rice-ratooning-rapeseed” cropping systems, to provide a theoretical basis for the further promotion and application of this model. Experiments were conducted in the southern part of Hunan Province from 2023 to 2024. Three combinations were established, including the short-growth-period ratoon rice variety ‘Lingliangyou 268’ + the medium-growth-period oilseed rape variety ‘Fengyou 737’, the medium-growth-period ratoon rice variety ‘Hui Liangyou 898’ + short-growth-period oilseed rape variety ‘Yangguang 131’, and medium growth period high-quality ratoon rice variety ‘Yexiangyou Lisi ’ + short-growth-period oilseed rape variety ‘Yangguang 131’. At the same time, two treatments were set, including different stubble heights for ratoon rice and different seeding rates for oilseed rape. The economic and ecological benefits of different combinations were systematically compared. The total annual growth duration of the three combinations ranged from 356 to 362 days, all of which could be normally cultivated in southern Hunan. The combination of short-growth-period ratoon rice variety ‘Lingliangyou 268’ + medium-growth-period oilseed rape variety ‘Fengyou 737’ with a 30 cm stubble height had the shortest total annual growth duration (356 days). In terms of economic benefits, the short-growth-period ratoon rice variety ‘Lingliangyou 268’ + medium-growth-period ‘Fengyou 737’ combination yielded the highest net profit at 26945 yuan/hm², which was 23.74%-27.47% higher than other combinations. This was primarily attributed to lower input, higher output, and a benefit-cost ratio 11.05%-13.02% higher than other combinations. Regarding the effects of rape seeding rate and rice stubble height, both varieties showed that doubled seeding rate increased total cost but resulted in a higher net profit. The short-growth-period ratoon rice variety ‘Lingliangyou 268’ + medium-growth-period oilseed rape variety ‘Fengyou 737’ combination with a 30 cm stubble height and doubled rape seeding rate achieved the highest net profit of 28357 yuan/hm², exceeding other treatments by 4.47%-54.47%. Regarding ecological benefits, methane emissions from the main crop of the ratoon rice varieties differed. The short-growth-period ratoon rice variety ‘Lingliangyou 268’ exhibited the lowest total methane emissions during the booting and heading stages. In terms of stubble height, the 30 cm stubble treatment resulted in lower methane emissions compared to the 15 cm stubble treatment, a trend consistent across all three varieties. In conclusion, the combination of short-growth-period ratoon rice variety ‘Lingliangyou 268’ + medium-growth-period oilseed rape variety ‘Fengyou 737’ combination with a 30 cm stubble height and doubled rape seeding rate demonstrated the best integrated economic and ecological performance. For the “rice-ratooning-rapeseed” system in southern Hunan, the optimal combination is the short-growth-duration ratoon rice variety ‘Lingliangyou 268’ paired with the medium-growth-duration oilseed rape variety ‘Fengyou 737’. Implementing a 30 cm stubble height for ratoon rice and a doubled seeding rate for oilseed rape within this combination can achieve high yields for both crops while reducing greenhouse gas emissions. Therefore, it is recommended to promote the application of the optimized combination in southern Hunan in order to maximize the comprehensive benefits of the “rice-ratooning-rapeseed” model and promote the sustainable development of agriculture.