Determination of the optimal fertilization method is crucial to maximize nitrogen use efficiency and yield of different rice cultivars. Side-deep fertilization with controlled-release nitrogen, in conjunction with machine transplanting and subsequent topdressing, was applied to Indica–japonica hybrid rice ‘Yongyou1540’ (YY1540) and indica hybrid rice ‘Tianyouhuazhan’ (TYHZ). Four nitrogen treatments were applied in 2018 and 2019: traditional nitrogen application with quick-release nitrogen (T1), single-dose deep fertilization at transplanting with 100% controlled-release nitrogen (T2), and deep fertilization of 70% controlled-release nitrogen and topdressing of 30% quick nitrogen at tillering (T3), or at panicle initiation (T4). Side-deep fertilization reduced the fertilizer application frequency without causing yield loss, T4 enhanced the yield of YY1540 by increasing the number of productive tillers and number of spikelets per panicle compared with T1, T2 and T3. The yield of TYHZ showed no significant difference among treatments. The T4 treatment decreased the number of tillers at the tilling peak stage and increased the percentage productive tillers and number of differentiated spikelets. Compared with the other treatments, T4 increased dry matter accumulation and leaf area index during panicle initiation and grain ripening, and contributed to enhanced nitrogen uptake and nitrogen utilization in YY1540. On average, nitrogen uptake and utilization in YY1540 were highest in T4, but no significant differences among treatments were observed in TYHZ. Dry matter accumulation and nitrogen uptake from panicle initiation to heading of YY1540 were correlated with number of spikelets per panicle, but no significant correlations were observed for TYHZ. Supplementary topdressing with quick-release nitrogen at the panicle initiation stage was required to increase yield of indica–japonica hybrid rice, whereas single-dose deep fertilization with controlled-release nitrogen is satisfactory for the indica hybrid cultivar.