In order to find out the relationship between root system of rice and its yield, a field plot research of different levels of fertilizer applications was conducted.Result showd that there was significant different existed between treatments, but there was no significant different existed between replications. Multiple rank test showed that the yield of plot with N, P, K was the highest and the yield of plot without fertilizer was the lowest.Research showed that plot yield was directly affected by the development of rice root system, besides fertilizer, the number of short root, long rooth had the greatest influence on yield and the amount of bleeding had the least influence through regression analysis.Reseacrch also showed that one of the key measure to get hight yield of rice is to promote root system development though fertilizer application control.