Wheat–maize rotation is a widely used planting pattern in oasis-irrigated areas in Northwest China. Although this planting pattern has the advantage of breaking the barrier of continuous cropping to some extent, it also presents some problems, such as large evaporation and prominent soil degradation during the fallow period, which seriously restricts the improvement of crop yield. Planting green manure (GM) after wheat and returning it to the field can effectively improve soil physicochemical properties, regulate the photosynthetic characteristics of subsequent crops, and promote crop yield. However, the photosynthetic physiological mechanism of crop yield improvement under different green manure return methods (GMRM) remains unclear. Therefore, by exploring the relationships among soil moisture and temperature environment, maize root structure, photosynthetic characteristics, fluorescence characteristics and yield under different GMRM, this study aims to provide a theoretical basis for clarifying the photosynthetic physiological mechanism of GMRM to improve maize yield. A three-year field experiment was conducted at a research station in the Shiyang River Basin (Gansu, China). Five treatments were involved in this study: (i) conventional tillage without GM (CT), (ii) no-tillage with total GM mulching (NTG), (iii) no-tillage with removal of aboveground GM (NT), (iv) tillage with total GM incorporation (TG), and (v) tillage with only root incorporation (T). Results showed that the NTG and TG significantly increased soil water content (SWC) in 0–110 cm soil layer, soil temperature (ST) of maize seedlings (V3) to jointing stage (V6), canopy cover (CC), leaf stay-greenness (SG), root length (RL), net photosynthetic rate (P_n), transpiration rate (T_r), actual photochemical efficiency of PSII (ΦPSII), maize biomass, and grain yield (GY) compared with CT. In addition, NTG and TG significantly decreased the ST of maize from the big trumpet stage (V12) to the blister stage (R2), and the dissipation of excess energy (NPQ), compared with CT. GM’s return to the field could improve root structure and canopy coverage of maize mainly by improving soil water content. The optimization of maize root structure and canopy coverage increased the maize chlorophyll content (SPAD) value and promoted P_n. The increase in P_n inhibits the increase in NPQ, thus promoting the activation of ΦPSII. The increase in ΦPSII promoted the increase in maize biomass, ultimately leading to an increase in maize GY.