In order to explore the effects of different irrigation methods on the physiological characteristics of mulch-free cotton in southern Xinjiang, the following experiments were carried out: (1) Different irrigation amount test: 300, 375, 450, 525, and 600 mm (represented by W1, W2, W3, W4, and W5) and a control (450 mm for film-covered cotton, represented by WCK) were set. (2) Drip irrigation frequency test: drip irrigation 12, 10, 8, and 6 times during the growth period (expressed by P12, P10, P8, and P6). Soil water dynamics, root distribution dynamics, chlorophyll fluorescence, leaf area index (LAI), SPAD (chlorophyll density), stress enzyme activities, and MDA (malondialdehyde) content were observed. The results showed that the average maximum change range of soil water content in the cotton field without film mulching was ��17.7%, which was 1.35 times higher than that in the cotton field with film mulching. Compared with cotton with film mulching, the root distribution characteristics of mulch-free cotton in the surface soil (0-20 cm) and the periphery (30 cm from the main root) decreased by 33.55-74.48% and 14.07-102.18%, respectively, while the root distribution characteristics in the deep layer (40-60 cm) increased by 49.62-242.67%, its average leaf green fluorescence parameters decreased by 9.03-50.44%, the activities of protective enzymes (SOD: superoxide dismutase, POD: peroxidase) decreased by 3.36-3.58%, the SPAD value decreased by 5.55%, and the MDA content increased by 3.17%, indicating that mulch-free cotton reduced the physiological function of cotton leaves, and the yield decreased by 42.07%. In the mulch-free treatments, the average root growth indexes were W2 > W3 > W4 > W5 > W1 and P12 > P10 > P8 > P6, and there was little difference between W2 and W3 and P12 and P10. With the increase in irrigation water and irrigation frequency, the initial fluorescence (F) of leaves in each period of mulch-free cotton showed a downward trend, and the maximum fluorescence (F), variable fluorescence (F), maximum photochemical efficiency (F/F), potential photochemical activity of PS II (F/F), electron transfer of PS II (F/F), and photosynthetic performance index (PIABS) showed an upward trend. In all water treatments, W3 and P12 had the highest SPAD value, protective enzyme activity, and the lowest MDA content, which was significantly different from other treatments except W4 and P10. The yield order of different treatments was W3 > W4 > W5 > W2 > W1, and the difference between W3 and W4 was not significant, but significant with W2 and W1. The irrigation frequency test was P12 > P10 > P8 > P6, and there was no significant difference between P12 and P10. We find that in the mulch-free treatment, all indicators of W3, W2, P12, and P10 were relatively high. It can be concluded that no mulching has a certain impact on cotton root distribution and leaf physiological function. When the irrigation amount is 450-525 mm and irrigation times is 10-12, it is beneficial for promoting root growth and plays a role in leaf physiological function, and the water use efficiency (WUE) is high, which can provide reference for the scientific water management of mulch-free cotton in production practice.