Background: Nutrient balance in rice paddy fields can change under different tillage management practices; however, the extent of the change may differ for various rice varieties. A field experiment was conducted over 2 successive years to clarify the effects of no-till and rice varieties on the apparent balance of nitrogen (N) and phosphorus (P). Four treatments: no-till/japonica rice (NTJ), no-till/glutinous rice (NTG), conventional tillage/japonica rice (CTJ), and conventional tillage/glutinous rice (CTG) with three replicates of each were established to test the hypothesis that no-till and japonica rice can improve the apparent balance of nutrients. Results: The tillage method and rice variety had interactive effects on the apparent balance of N and P. After the 2-year experiment, total N and P pools in the 20 cm surface soil layer were highest under the NTJ treatment (4757.0 kg N ha −1 , 2428.5 kg P ha −1) and lowest under the CTG treatments (4726.3 kg N ha −1 , 2412.0 kg P ha −1). Under no-till conditions, japonica rice had higher grain yield but lower straw biomass than that of glutinous rice. NTG treatment significantly increased the N and P content in rice grains and straw. The environmental losses of N and P in the rice fields mainly occurred during the rice season. Based on nutrient balance estimation, N losses in the NTJ, NTG, and CTJ treatments were reduced by 15.03 kg N ha −1 , 11.55 kg N ha −1 , 6.72 kg N ha −1 , respectively, as compared with that of the CTG treatment. The corresponding P losses were reduced by 8.02 kg P ha −1 , 7.84 kg P ha −1 , and 3.96 kg P ha −1. In terms of economic benefits, NTJ also resulted in the highest actual income (2724.25 US dollars) and the highest ratio of production investment (6.40). Conclusion: No-till was more likely to maintain soil N and P nutrients than conventional tillage, and this advantage was most significant when planting japonica rice. In addition, no-till was conducive to N and P uptake by rice, but only japonica rice exhibited increased grain yield. Consequently, the NTJ treatment was recommended to improve the N and P balance.