In order to explore a suitable application mode of bio-organic fertilizer and chemical fertilizer for paddy fields, the effects of application modes with different bio-organic fertilizer to chemical fertilizer ratios on effective soil nutrient accumulation, rice growth and yield in water-saving irrigated paddy fields were investigated by plot experiments. Five treatments were set for the observation, including full chemical fertilizer (T0), 75% chemical fertilizer with 25% bio-organic fertilizer (T1), 50% chemical fertilizer with 50% bio-organic fertilizer (T2), 25% chemical fertilizer with 75% bio-organic fertilizer (T3) and full bio-organic fertilizer (T4). The results showed that the soil organic matter content increased after harvest in all treatments, with an increment of 21%-29%； furthermore, the effective phosphorus and fast-acting potassium contents of the soil were increased by 2.1%-18.9% and 6.0%-11.7%, respectively, with the application of bio-organic fertilizer. Compared with the T0 treatment, the application of bio-organic fertilizer advanced the tillering time of rice, improved the leaf area index of rice up to 13.5%-40.5%, and increased the number of grains in the spike, the seed setting rate and the thousand-grain weight of rice. Among the treatments with bio-organic fertilizer, the yield of rice in the T3 and T4 treatments was increased by 7.0% and 1.7%, respectively, and the final benefit of T3 treatment was significantly increased by 8.7% (P<0.05) in particular. It can be seen that the treatment of 25% chemical fertilizer with 75% bio-organic fertilizer has a better promotion effect on the accumulation of effective nutrients and rice growth in water-saving irrigated paddy fields.