Field performance of insect-resistant transgenic rice needs to be meticulously evaluated before it is commercialized. To our knowledge, little information are available about the field performance of Bt rice with cry1C* or cry2A* genes under different nitrogen (N) levels. Field experiments were conducted to investigate the yield performance and yield-related traits of Bt-MH63 under three N levels (0, 150 and 195 kg N ha−1). The results showed that MH63 (cry1C*) had lower grain yield than MH63 at all N levels due to the reduced grain filling percentage. Furthermore, MH63 (cry1C*) as compared with MH63 had lower dry matter translocation efficiency and higher reservation of soluble sugar in stem and sheath at mature at all N levels. At 0 kg N ha−1, grain yield and internal N use efficiency (IEN) of MH63 (cry2A*) were significantly lower than those of MH63 possibly due to the leaf premature aging of MH63 (cry2A*). In contrast, there were no significant differences in the grain yield and leaf senescence between MH63 (cry2A*) and MH63 at 150 and 195 kg N ha−1. The results indicated that the incorporation of cry1C* or cry2A* caused varying degrees of yield reduction in rice due to different agronomic reasons.