Machine-transplanted rice with side-deep fertilization (MRSF) is a recommended strategy to reduce labor cost and nitrogen (N) fertilizer loss in sustainable double-cropping rice production in China. However, the effects of MRSF on double-cropping rice profitability and agronomic traits are unclear. Here, experiments were conducted in two sites at Dongting Lake to determine the yield and economic benefits of MRSF and the optimal N application rate. Six fertilization treatments for early- and late-season rice at various N rates (0/0, 90/99, 105/116, 120/132, 135/149, and 150/165 kg N ha⁻¹) were tested. The grain yield of early-season rice (ESR) was the highest (8.7 t ha⁻¹) under 70 % deep fertilization (DF), whereas that of late-season rice (LSR) was the highest (6.1 t ha⁻¹) under 80 % DF treatment in Miluo. The grain yield of ESR and LSR (7.5 and 7.9 t ha⁻¹, respectively) were the highest under 80 % DF treatment in Yiyang. Compared with conventional fertilization (CF), MRSF significantly enhanced grain yield by 0.5 %–20.2 % and 5.3 %–15.0 % in Miluo and Yiyang, respectively. The high grain yield under MRSF can be attributed to higher leaf area index, chlorophyll content, nutrient uptake, biomass accumulation, and spikelet number per m². Relative to CF, MRSF increased the panicle bearing tiller rate by 8.4 %–24.6 % (Miluo) and 3.3 %–12.2 % (Yiyang), thereby improving dry matter accumulation and nutrient uptake. Furthermore, the economic benefit under MRSF increased by 9.9 %–31.8 % (Miluo) and 15.0 %–25.7 % (Yiyang) compared with that under CF. N reduction in the MRSF treatments resulted in fewer effective panicles than the 100 % DF treatment. Improved yield and nutrient uptake in double-cropping rice were associated with deep fertilizer placement rather than N application rate. The number of filled grains per panicle had the strongest influence on ESR and LSR grain yield. Overall, MRSF is recommended as an alternative approach to increase grain yield, profitability, and agronomic traits while lowering the N application rate in the double-cropped rice systems near Dongting Lake, southern China.