Abstract: In order to develop organic rice and increase paddy soil fertility by clover-organic rice rotation, the authors studied the effect of N, P and K on the growth of clover nitrogen-fixing rhizobia and soil fertility after plantation, aimed to provide reference for the reasonable plantation of clover and soil fertility increase. A two-year experiment was conducted from 2012 to 2013, clover was cultivated after rice every year and different levels N, P and K fertilizer were applied before winter, CK treatment was without fertilizer. The effects of different fertilizers and different application amounts on clover yield, nitrogen-fixing rhizobia quantity, nitrogen-fixing rhizobia weight and soil fertility after plantation were analyzed. The results showed that the application of N, P and K in the earlier stage had significant effect on the growth of clover, when the nitrogen application amount was 75 kg/hm² (N 46%), clover yield, nitrogen fixing rhizobium quantity and weight reached the maximum. Soil nitrogen content after plantation increased with the increase of the application amount of nitrogen fertilizer, while phosphorous and potassium content decreased and then increased with the increase of the application amount. The content of available P increased with the increase of N and P application amount and had significant change with the application of K. The content of available K first increased and then decreased with the increase of N and P application amount, when N was 150 kg/hm² (N 46%) and P was 300 kg/hm² (P₂O₅ 12%), the available K content reached the maximum. Soil organic matter content increased with the increase of fertilizer application amount. So, N, P and K should be applied in the earlier stage in clover plantation, which could increase clover yield and soil fertility.