The soil water storage, growth development, biomass and yield in maize/soybean intercropping system under different separation methods were measured to analyze the resource competition of the intercropping crops. The treatments included no shoot or root separation (T₁), shoot and root separation (T₂), only root separation (T₃), and only shoot separation (T₄). Results indicated that compared to others, the average soil moisture content in the 0-120 cm soil layer decreased by 3.1%-12.9% in maize line, and by 2.8%-12.5% in soybean line for T₁. Compared to T₁, maize growth stage in T₂, T₃ and T₄ came late, and the plant height, leaf area and cumulative total biomass, yield and yield components all decreased, while the trends found for soybean were the opposite. In summary, the changes of crop growth and yield in the maize/soybean intercropping system were driven by the interactions of above and belowground parts, and the belowground part played a more important role.