Agroforestry, as a phytoremediation measure, shows great potential for mitigating land degradation by constructing multidimensional and efficient agroforestry composite systems through regulating the microenvironment of agroforestry sites and improving soil properties. However, the effects of different agroforestry composite management modes on saline soils and the interactions between soil–plant systems under salt stress conditions in coastal areas remain largely unexplored. In this study, two salt‐tolerant tree species (Sapium sebiferum (Linn.) Roxb and Zelkova serrata (Thunb.) Makino) and four crop species (Medicago sativa, Sesbania cannabina, Sorghum bicolour, and Avena sativa) were selected for intercropping in eight composite patterns via field experiments, with dynamics of soil physicochemical properties and crop photosynthesis observed. The results showed that treatments intercropped with M. sativa had the highest soil bulk density range (1.41–1.48 g cm−3). The dynamics of topsoil (0–10 cm) chemical properties showed similar change patterns among treatments, whereas those of the 10–40 cm soil chemical properties (especially soil pH, soil organic matter [SOM], and total nitrogen [TN]) showed heterogeneity. Moreover, planting S. sebiferum (L.) Roxb under the same crop conditions increased tree height growth rate and survival rate by 75%–114% and 14%–33%, respectively, relative to planting Z. serrata (T.) Makino. Furthermore, a significant negative correlation was observed between soil moisture with crop intercellular CO2 concentration (λ = −0.77), while significant positive correlations were found between crop net photosynthetic rate (Pn) with soil TN (λ = 0.71), as well as SOM with atmospheric CO2 content (λ = 0.72). Structural equation modeling showed significant direct effects between tree height growth rate with soil TN and SOM. Soil moisture (λ = 0.47) and tree height growth rate (λ = 0.53) were dominant drivers of crop Pn. Our findings provide useful information for the prevention of coastal saline soil degradation and sustainable development of agroforestry.