In order to formulate a reasonable water input model for cotton fields in southern Xinjiang, scientific and rational fertilization, reduce soil carbon leaching, and improve soil carbon sequestration capacity, the undisturbed soil column leaching test was used to simulate the current field management method in the study area. Two methods of drip irrigation and flood irrigation were set up, and three irrigation and three nitrogen fertilizer levels were used to carry out the undisturbed soil column leaching test. The results showed that the amount and mode of water and nitrogen input affected the distribution and leaching loss of organic carbon and inorganic carbon in soil. When the nitrogen application rate increased from 270 kg·hm-2 to 450 kg·hm-2, the leaching loss of soluble organic carbon and soluble inorganic carbon increased significantly. When the water input increased from 6000 m3·hm-2 to 9000 m3·hm-2, the leaching loss of DOC and DIC increased significantly. The carbon leaching loss under drip irrigation was higher than that under flood irrigation. The leaching rates of DOC and DIC were the fastest under the conditions of high water ( 9000 m3·hm-2 ) and high fertilizer ( 450 kg·hm-2 ). It shows that water and nitrogen input and irrigation methods are important factors affecting soil carbon leaching. In the case of excessive water input, long-term high-frequency irrigation is the main factor affecting carbon leaching.