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Dry direct-seeded rice sown by multifunctional seeders (MS-DDSR) has received increased attention for its high efficiency. Wheat straw returning is widely used as an important agricultural practice because it is the simplest and quickest approach to dispose of wheat straw and also improve soil quality. The study determined whether MS-DDSR after wheat straw returning could obtain a high yield and whether early nitrogen (N) application could compensate for the negative effects caused by returned wheat straw. Field experiments were performed in a split-plot design. Main plots were comprised without wheat straw returning (S0) and wheat straw returning (S1). Split plots consisted of three plots with early N application treatment: 65 (N1), 95 (N2), and 125 (N3) kg N ha−1 at 0 and 20 days after sowing. S1 reduced yield, N uptake, and biomass accumulation in MS-DDSR compared to S0 because S1 negatively affected the seedling roots growth, seedling establishment, and tillering capacity of MS-DDSR. The positive interaction between wheat straw returning and early N on yield, biomass accumulation, and N uptake was likely related to the positive interaction on spikelet number per panicle, total spikelet number, and biomass accumulation after the stem elongation stage. These findings demonstrate that wheat straw returning led to poor seedling establishment and yield loss for MS-DDSR, but these negative effects could be compensated for by an appropriate increase in early N application, based on the locally recommended N application protocols.