In this study, a typical apple–soybean intercropping system was used to analyze the effects of different soil water and heat regulation modes on the spatial distribution of the soil water content (SWC), photosynthetic physiological characteristics, and growth. Three maximum irrigation levels [50% (W1), 65% (W2), and 80% (W3) of field capacity (FC)] and two mulching intervals [from seedling to podding stage (M1) and during the full stage (M2) of soybeans] were tested. The results showed that the SWC of W3M2 was the highest, while the W2M1 and W1M2 treatments used more deep soil water. Irrigation increased the chlorophyll content, net photosynthesis, and transpiration rate of leaves in the agroforestry system. In addition, the net photosynthetic rate of leaves under the W2 irrigation level increased after mulch removal in the later growth stage. At W1 and W2 irrigation levels, the soybean yield of half-stage mulching was 0.85–15.49% higher than that of full-stage mulching. Multiple regression analysis showed that grain yield under the W3M2 treatment reached the maximum value of the fitting equation. The photosynthetic rate, water use efficiency, and grain yield under W2M1 reached 71–86% of the maximum value of the fitting equation, with the largest soil plant analysis development value. To effectively alleviate water competition in the apple–soybean intercropping system, our results suggest adoption of the 80% FC upper irrigation limit (W3) combined with soybean M2 treatment in young apple trees–soybean intercropping system during water abundant years. In addition, adoption of the 65% FC upper irrigation limit (W2) combined with the soybean M1 treatment in water deficit years could effectively improve soil water, heat environment, and promote growth.