To explore the effect of marginal effect on physiological development of intercropping cotton, we used sufficient irrigation and deficit irrigation to analyze the physiological indexes and crop yields of four-row intercropping cotton. The cotton near the jujube trees is named as Row D1, and other rows as Row D2, D3 and D4, respectively. The results showed that under sufficient irrigation conditions, the physiological indexes and crop yields of intercropping cotton were significantly higher than those of single cropping, and intercropping was beneficial to cotton growth and development. Even under water deficit conditions, crop yields still increased by 2.53%, because the intercropping changed the spatial distribution of soil moisture, triggering interspecific competition and complementary mechanisms. Among the four rows of cotton, cotton of Row D1 was obviously affected by the competition with the jujube trees and the shading effect. Its physiological indicators and crop yield were slightly lower than Row D2, but still higher than the single cropping. The cotton growth of Row D2 was the best among the four rows, with the largest net photosynthetic rate and the highest crop yield. Because Row D3 and D4 were far away from the trees, which were restricted by intra-species competition, so the physiological indicators were only slightly higher than single cropping. However, there was no significant difference in the SPAD of singlecropping cotton, indicating that the shading of the jujube trees had a weak effect on cotton chlorophyll. After applying water deficit in the intercropping cotton, Row D1 and D2 were less affected, and the plant physiological indicators and crop yields even increased slightly. The plant height and leaf area index of Row D3 and D4 decreased by 20.69% and 4.89% respectively, and the crop yield reduced by about 11%. Therefore, the intercropping will cause a strong marginal effect, resulting in significant differences in the physiological characteristics of the four rows of cotton. The closer to the jujube trees, the higher the impact degree and the stronger the ability of water stress resistance of the cotton, but it is also susceptible to interspecies competition and the shading effect of jujube trees.