Rice is an important staple food around the world, the cultivation as sustainable agriculture and food supply are key to achieving the Sustainable Development Goals (SDGs) of 2030. In order to analyze the sustainability of the rice paddy ecosystem, a comparative study was carried out during the rice growing season between paddies with conventional agriculture (CA) and ecological agriculture (EA), integrating analysis of physico-chemical characteristics of soil and soil pore water, pesticide residues, acute toxic effects and potential ecological risk, as well as aquatic invertebrate community structure dynamics. Our study found that total carbon and nitrogen present in soil were significantly higher in CA than in EA, while opposite results were found in soil pore water, implying the improvement on soil properties in EA. Neonicotinoid pesticides (thiamethoxam and thiacloprid) were still detected in EA, although no pesticides were applied after conversing CA to EA. Additionally, toxic effects to zebrafish embryos with a peak toxicity in summer (July, LC50 = 55.26 mg soil equivalent/L) were also found in EA, which was lower than in CA. The dynamics of the aquatic invertebrate community structure were correlated with the toxicity results, with higher diversity recorded in EA. Therefore, for the purpose of ecosystem sustainability, the long-term implementation of EA is highly recommended.