Rice-crab culture is the characteristic rice ecological breeding model used in the Panjin area of Liaohe River Basin, China, and it can improve the ecological environment and create increased economic benefits. From a food perspective, both rice yield and quality, which are closely related to the fertilization mode, should be considered. However, the effect of different fertilization modes on rice quality has not been comprehensively investigated in this co-culture system. This study investigated the effects of three fertilization modes(FP1, FP2, and OPT) divided according to different fertilization types and methods on rice yield and quality, and set up a non-fertilized control group. In the rice-crab culture system, FP2 used fewer fertilizers and had a lower economic cost, and the yield was only slightly less than that of OPT(highest yield) but there was no statistical difference. FP2 elicited the best appearance quality and better cooking and eating quality among all treatment modes. Compared with CK, three fertilization modes significantly increased the protein content in rice and decreased the amylose content, which would lead to the deterioration of rice eating quality. However FP2 had the least protein increase and the least amylose reduction. There was no significant change in crude fat and starch content. Therefore, the FP2 fertilization mode was the best choice for the rice-crab culture system, as it significantly improved rice yield and increased rice quality at a relatively low cost.