The decrease in reproductive organ biomass is a principal constraint for cotton yield under conditions of limited nitrogen (N). We aimed to alleviate this challenge by reasoning N applications in order to exploit the photosynthetic potential and improve the distribution of photosynthates. Cotton crops were grown in a two-year field experiment (2019–2020) under N-reduced cultivation (23.9 ×104 plants ha−1, 76 cm row spacing, and applied 240 kg N ha−1), N fertigated with five ratios at squaring (SQ): flowering to peak boll (FPB): late peak boll (LPB), i.e., 4:6:0 (N460), 3:6:1 (N361), 2:6:2 (N262, Control), 1:6:3 (N163) and 0:6:4 (N064). Impacts of N treatment (ratio) were investigated for leaf area, chlorophyll content, photosynthetic characteristics, photosynthetic N use efficiency (PNUE), sink capacity characteristics, and biomass accumulation. Correlations between traits were also analyzed. Compared with conventional N262, N064 increased reproduction organs biomass by 10.1–10.3%. Furthermore, during the LPB to boll opening stage, N064 increased fruit branch leaf area by 1.4–26.8%, chlorophyll content by 6.4–27.6%, net photosynthetic rate by 15.1–35.9%, actual photosynthetic efficiency by 14.4–41.6%, photochemical quenching by 18.0–57.7%, PNUE by 15.7–41.0%, and sink capacity by 6.7–10.5%; while it decreased foliage branch leaf area by 13.1–22.4% and chlorophyll a/b by 6.1–10.2%. Overall, late N fertilization was an effective strategy to (1) retain post-flowering photosynthetic capacity by developing more fruit branch leaf area with higher chlorophyll content and lower chlorophyll a/b, (2) optimize sourcesink relationship by increasing boll capacity, and (3) increase biomass in reproductive organs, thus enhancing sustainable and efficient production of cotton under N-reduced cultivation in arid regions.
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