Abstract: In order to reveal the comprehensive effect of traditional chemical fertilizer and organic planting models in southern China region, a field trail was conducted to monitor the greenhouse effect, rice economic profit, 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 to the chemical fertilizer application, the greenhouse effect and its 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 with cow dung compost application (223.4~365.98 kg/hm²) than that with chemical fertilizer application (150.3~216.7 kg/hm²) in early and late rice paddy soils (p < 0.05). Though rice yield with cow dung compost application decreased by 7.66%~16.9% relative to that with chemical fertilizer application, the output value and profit of rice increased by 66.3%~84.7% and 92.9%~117.4%, respectively. This was related to the twice price of organic rice than ordinary rice. The content of gram-positive (G⁺) bacteria phospholipid fatty acids (PLFAs) in early rice paddy soil with cow dung compost application significantly decreased by 41.4% (p < 0.05) compared to that with chemical fertilizer application, leading to the decrease in the ratios of G⁺ to G^- bacteria and bacteria to fungi. While no significant difference of each microbial group-derived PLFA was found between chemical fertilizer and cow dung compost application in late rice paddy soil. Under the suitable environmental condition (ample water and light) in early rice paddy soil, the microbial network complexity with cow dung compost application decreased relative to that with chemical fertilizer application; while it showed the reversed trend under the drought stress condition in late rice paddy soil. This study revealed the vital role of organic farming mode in rice economic profit increase, soil quality improvement, and soil microbial homeostasis sustainment, which could provide references for organic farming exploration in southern China region.