Abstract: In order to reveal the comprehensive effects of conventional chemical fertilizer and organic fertilizer application models in southern China, a field trail was conducted to monitor the greenhouse effect, rice economic profits, and microbial characteristics in early and late rice paddy soils under the application of chemical fertilizer and cow dung compost. The results showed that compared with those after chemical fertilizer application, the global warming potential and greenhouse gas emission intensity after cow dung compost application in early and late rice paddy soils increased by 40.6%−61.7% and 67.6%−75.2%, respectively (P<0.05). This was ascribed to the higher cumulative methane emission under cow dung compost application (223.4−365.98 kg∙hm⁻²) than that under chemical fertilizer application (150.3−216.7 kg∙hm⁻²) in early and late rice paddy soils (P<0.05). Though rice yield under cow dung compost application decreased by 7.66%−16.9% compared with that under chemical fertilizer application, the output value and profit of rice increased by 16.4%−29.3% and 30.8%−49.8%, respectively. This was related to the higher price of organic fertilizer-planted rice than ordinary rice. The content of phospholipid fatty acids (PLFAs) from gram-positive (G⁺) bacteria in the early rice paddy soil under cow dung compost application decreased by 41.4% (P<0.05) compared with that under chemical fertilizer application, leading to the decrease in the ratios of G⁺ to G⁻ bacteria and bacteria to fungi. While no significant difference in each microbial group-derived PLFA was observed between chemical fertilizer and cow dung compost application in the late rice paddy soil. Under the suitable environmental conditions (ample water and light) in the early rice paddy soil, the microbial network complexity under cow dung compost application decreased compared with that under chemical fertilizer application, while it showed the reversed result in the late rice paddy soil under drought stress. This study reveals the vital role of organic fertilizer application model in rice economic profit increasing, soil quality improvement, and soil microbial balance sustainment, providing references for agricultural planting model exploration in southern China.