Background: Agrochemicals, such as pesticides and fertilizers used in the current conventional agriculture (CA), have contaminating effects on environments as well as food, which pose significant risks to non-target organisms and even human health. Under these environmental pressures, ecological agriculture (EA), using organic fertilizer for crop growth, was developed without pesticides to substitute CA gradually worldwide. However, EA has still not become popular in the Chinese mountain area. To identify the major factors that influence the application of EA, rice cultivation between EA and CA was compared by analyzing soil physical-chemical properties, and soil bacterial and plant diversity in Chongqing. Besides, in considering the economic benefits of small-scale paddy ecosystem, net present value (NPV) method was applied for quantification and evaluation between EA and CA. Results: The rice yield of EA (3700 kg/ha) was significantly lower than that of CA (7500 kg/ha). Soil total nitrogen (TN, 2.24 ± 0.16 g/kg) and available potassium (AK, 70.67 ± 9.88 mg/kg) in CA were higher than those in EA, with amounts of 1.45 ± 0.18 g/kg (TN) and 54.00 ± 5.89 mg/kg (AK). Soil organic matter (SOM) of CA (55.6 ± 5.8 g/kg) was distinctly higher than that of EA (24.4 ± 1.43 g/kg), whereas pore water DOC concentration in EA (71.11 ± 7.28 mg/L) was higher than that in CA (61.07 ± 6.61 mg/L). Plant richness, bacterial diversity of ACE and Chao1 in EA were significantly higher than in CA (P < 0.05). The net present value (NPV) of EA was 3.72 CNY/m 2 , which was higher than that of CA (2.98 CNY/ m 2). Conclusions: The relative high amounts of AP, pore water DOC and bacterial diversity revealed the improvement of soil properties by EA. Limitations on N and AK may be responsible for the low yield in small-scale EA of the current study. In addition, economic benefits, plant richness and bacterial diversity suggested EA application in China as well as worldwide to facilitate the sustainable development of the agroecosystem. However, animal diversity and quantification on economic benefits of ecological services should be considered in further research to promote the sustainability development of the agroecosystem.