•The grain yield of common buckwheat was significantly correlated with photosynthetic capacity, and agronomic traits.•N fertilizer and planting density had significant effects on the photosynthetic capacity, agronomic traits, and yield of common buckwheat.•The combination of N fertilizer of 45 kg ha−1 and 90 plants m−2 is recommended for enhancing the yield of common buckwheat. Nitrogen fertilizer and planting density are two crucial factors that affect the yield of common buckwheat (Fagopyrum esculentum M.). Youqiao2, a common buckwheat cultivar with high photosynthetic capacity and planted widely in local production was used to investigate the effects of nitrogen fertilizer and planting density on the leaf photosynthetic characteristics, agronomic traits, and grain yield in common buckwheat by a split plot design. The main plots were assigned to three nitrogen fertilizer rates: 0, 45, and 90 kg ha−1, and the subplots were assigned to three planting densities: 60, 90, and 120 plants m−2. Results showed that the grain yield was significantly and positively correlated with net photosynthesis rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), stomatal limitation value (Ls), chlorophyll content (SPAD value), leaf area index (LAI), plant height, stem diameter, branch number, internode number, grain number per plant, and 1000-grain weight, while significantly and negatively correlated with intercellular CO2 concentration (Ci) and water-use efficiency (WUE). The Pn, Gs, Tr, Ls, SPAD, LAI, grain yield, stem diameter, branch number, internode number, grain number per plant, and 1000-grain weight increased and then decreased with the increase of nitrogen fertilizer and planting density, and their maximum values appeared in the nitrogen fertilization of 45 kg ha−1 and planting density of 90 plants m−2 treatment. The Ci and WUE decreased and then increased with the increase of nitrogen fertilizer and planting density, and their minimum values appeared in the nitrogen fertilization of 45 kg ha−1 and planting density of 90 plants m−2 treatment. The plant height increased with the increase of nitrogen fertilizer, while decreased with the increase of planting density. These results suggested that nitrogen fertilizer and planting density had significant effects on the leaf photosynthetic capacity, agronomic traits, and grain yield of common buckwheat, and the combination of nitrogen fertilization of 45 kg ha−1 and planting density of 90 plants m−2 is recommended for common buckwheat planting.