Maize shading affects the growth and development of soybean in maize soybean intercropping systems. Two different soybean varieties were (ND12, high shade-tolerant, and GX3, low shade-tolerant) relay intercrop with maize in different (T1, double row, and T2, single row) relay strip intercropping systems, and the results of the both planting arrangements of strip intercropping system were compared with the sole planting system of soybean. The results showed that shading reduced the content of photosynthetic pigment per unit area of soybean leaf, Fv/Fm, ΦPSⅡ, and Fv/Fo of ND12 and GX3 under T1 and T2. Moreover, T1 and T2 also decreased the density and size of stomata, leaf thickness, palisade tissue thickness of the tissue, and the size of the chloroplast and starch grains, while increased the thickness of the granum lamellae in both varieties of soybean. Nevertheless, the leaf area, aboveground biomass, photosynthetic capacity, photosynthetic organs measured morphological and architectural indices were found maximum in ND12 compared to GX3 in all planting patterns.