In this study, three japonica rice varieties—Nanjing 9108, Jiahua 1 and Wuyunjing 29—were supplied with different levels of nano-foliar selenium fertilizers (0, 40 and 80 kg Se ha−1) under field conditions. Their rice yield and absorption, accumulation, transportation and utilization of selenium were studied to find suitable selenium-rich rice cultivars and optimal selenium supply levels, while providing references for the development of selenium-rich rice. On an average basis, the Nanjing 9108, Jiahua 1 and Wuyunjing 29 yielded 8755 ± 190, 8200 ± 317 and 9098 ± 72.7 kg ha−1, respectively. The selenium content in polished rice of the three rice varieties is between 0.210 and 0.933 mg kg−1. When 40 g Se ha−1 nano-selenium fertilizer was used, the selenium accumulation in the shoots of Nanjing 9108, Jiahua 1 and Wuyunjing 29 was, respectively, 11.4 g Se ha−1, 12.3 g Se ha−1 and 12.2 g Se ha−1, and when 80 g Se ha−1 selenium fertilizer was applied, the total selenium accumulation of three rice varieties was, respectively, 2.45, 1.75 and 2.40 times that of 40 g Se ha−1 selenium fertilizer. No evident diversity was observed in the selenium transport coefficient and the apparent utilization rate of selenium among the three varieties. The three rice varieties in this experiment had a strong selenium enrichment capacity, and they could be planted as selenium-enriched and high-yield rice varieties. Further, the amount of selenium fertilizer should not exceed 40 g Se ha−1.