By way of using different kinds of fertilizer in the system of rice intensification,the results have showed: under the same condition of cultivation and management, All fertilizers can enhance the number of tillering of rice. The number of tillering in rice of maximum is treatment 3(organic fertilizer). Maximum effective tiller rate is treatment 6(microbes activity fertilizer+organic fertilizer+fertilizer). The root activity of treatment 6 is the highest on heading stage of rice,,the grain yield of treatment 6is higher than other treatments. Using different kinds fertilizer, the effects of grain quality are different under SRI condition. By applying organic fertilizer, it can improve machining quality of rice (especially increase milled rice and head mill rice.) and decrease the percentage of chalky kernel and chalkiness. It can decrease amylose content of rice that organic fertilizer coordinate using fertilizer. It was obvious to improve grain quality that organic fertilizer coordinated using fertilizer or microbes activity fertilizer coordinated organic fertilizer and fertilizer.