Abstract: This study investigated the effects of calcium–nitrogen interaction on soybean yield formation, physiological traits, nutrient uptake, and nitrogen use efficiency. A two-factor field experiment was conducted in 2024 in Yuanyang County, Henan Province, with three nitrogen rates (0、75、150 kg·hm⁻²) and two calcium rates (0 and 150 kg·hm⁻²). Yield performance, leaf photosynthetic physiology and microstructure, nutrient accumulation and translocation, and soil nitrogen availability were systematically analyzed. The results showed that calcium–nitrogen interaction significantly enhanced soybean yield, nitrogen and calcium accumulation, and fertilizer utilization. Compared with Ca0N0, the Ca150N75 treatment increased yield, aboveground nitrogen accumulation, and calcium accumulation by 49.82%, 29.54%, and 125.04%, respectively, and achieved the highest nitrogen use efficiency (49.28%), agronomic efficiency (8.47 kg·kg⁻¹), and partial factor productivity (37.14 kg·kg⁻¹). Calcium–nitrogen interaction significantly promoted nitrogen translocation and redistribution. Moreover, combined calcium and nitrogen application improved leaf anatomical structure and photosynthetic performance and increased soil total nitrogen, ammonium nitrogen, and nitrate nitrogen contents. Mantel analysis revealed significant positive correlations between calcium–nitrogen interaction and photosynthetic traits, nutrient uptake, and soil nitrogen availability (P < 0.05). Overall, appropriate combined calcium and nitrogen application (Ca150N75) effectively improves photosynthetic capacity, nitrogen utilization efficiency, and soybean yield, providing a scientific basis for green fertilization management.