Incorporating green manure is a vital strategy for optimizing cropping systems and improving soil quality. However, it is unclear whether the effects of different types of green manure on subsequent cotton yield and soil fertility improvement are uniform. This study evaluated the effects of three green manure incorporation treatments over a two-year cropping cycle (Chinese violet-cotton-Chinese violet-cotton (T1), rapeseed-cotton-rapeseed-cotton (T2), and ryegrass-cotton-hairy vetch-cotton (T3)) on cotton yield and yield components. These treatments were also compared with the winter fallow-cotton (T0) to analyze differences in soil nutrients and net ecological–economic benefits. No significant differences in cotton yield or yield components were observed among the green manure incorporation treatments. However, averaged across two years, T1 produced a seed cotton yield 8.1% higher than T2 and 3.9% higher than T3. T2 and T3 significantly enhanced soil alkali-hydrolyzed nitrogen, organic matter, and total humus content compared to T0. Notably, T3 increased these parameters by 18.7, 23.9, and 26.8%, respectively. Additionally, T3 achieved the highest net ecological–economic benefit, exceeding T0 by $405/ha. This study highlights the potential of green manure to enhance soil fertility and ecological–economic sustainability in cotton fields. Further research is required to evaluate its long-term benefits and broader implications for sustainable agriculture.