Traditional fertilization and irrigation methods have resulted in low nitrogen (N) use efficiency and large N loss. Reducing N fertilizer input is a necessary condition for environmental protection. We investigated the effects of different irrigation and fertilization on rice growth and soil N dynamics. Results showed that the growth of rice under two irrigation regimes was not significant, while the effect of fertilization on growth was significant. The combined application of organic and inorganic fertilizers was beneficial to the conversion of N in the soil, and reduced the N concentration in the paddy soil, as well as reduced the risk of N loss. Compared to the unfertilized control, the application of combined organic and inorganic fertilizers, as well as a controlled irrigation method, promoted N use efficiency, improved rice production, and decreased N pollution to the environment. Taking the indices of the growth of rice, nitrogen accumulation, nitrogen use efficiency into account, the combination of organic and inorganic fertilizer applications and controlled irrigation are recommended to be a proper irrigation and N application strategy for paddy soil and rice plants.