Increasing plant density can increase cereal crop yields. However, the physiological and anatomical mechanisms of grain yield increase at high plant densities in maize-based intercropping systems are not well understood. A two-year field experiment was conducted in 2018 and 2019 to investigate grain yield, photosynthetic characteristics, stomatal traits, and leaf anatomy of maize plants in an intercropping system with high plant densities. Two cropping patterns (monocropping and intercropping) and three plant densities (D1, 78,000 plants ha1; D2, 103,500 plants ha1; D3, 129,000 plants ha1) were arranged in a randomized block design. Increasing maize plant density significantly increased maize yield, and intercropping gave a significant yield advantage over monocropping under the same plant density. Intercropping combined with high plant density increased the leaf area and SPAD value of maize, increasing the photosynthesis rates after the harvest of pea. At the twelfth leaf stage, the stomatal density and stomatal area of intercrops combined with medium plant density increased by respectively 10.5% and 18.4% relative to their values for the corresponding density of monocrops. Although leaf thickness of maize was reduced by increasing plant density, the ch oroplast number and grana lamella number were higher in intercropping than in monocropping under different plant densities. These positive changes in leaf anatomy resulted in increased photosynthesis, suggesting a physiological basis for the increase in grain yield.