The evolution of pore structure and the mechanism of its influence on both soil moisture and solute breakthrough during the straw decomposition process were experimentally investigated. Treatments with straw application rates of 0t/hm2, 5t/hm2, 10t/hm2, and 15t/hm2 and decomposition time points of 0d, 30d, and 60d were set up for the CT tomography and breakthrough experiment. CT tomography was employed to visually quantify the evolution of soil pore structure, and the breakthrough experiment was employed to analyze the evolution of moisture-solute transport preferential flow pattern. The results showed that at the early stage of straw decomposition, features of soil pore/throat pathways were modified, which inhibited the moisture-solute transport. Field capacity and soil moisture content were increased, solute breakthrough was slowed down, and the preferential flow pattern was restrained with straw incorporation. Soil moisture and fertilizer can be effectively retained, consequently. As straw was decomposed to 60d, the pore/throat pathways were changed, and the preferential flow began to develop, but the soil moisture and fertilizer retention capacity were increased. At the initial stage of straw application of 5t/hm2, 10t/hm2, and 15t/hm2, compared with the CK group, the proportion of macropore volume was decreased by 7%, 14%, and 50%, the connected pore was decreased by 11%, 39%, and 66%, the surface moisture content was increased by 1%, 3%, and 6%. After 60d of decomposition, compared with group 0d, the proportion of macropore volume was increased by 331%, 200%, and 357%, the connected pores was increased by 33%, 84%, and 195%, the surface moisture content was increased by 6%, 5%, and 5%, and the solute collected was decreased by 55%, 76%, and 67% when completed breakthrough, respectively. Based on the Green-Ampt model and the exponential decay model, models for the estimation of saturated hydraulic conductivity were proposed with different straw application rates at different decomposition time points. It indicated that the saturated hydraulic conductivity was decreased after straw application and increased with straw decomposition. The most significant novelty lied in the fact that the features of different stages of straw decomposition were revealed, providing a basis for controlling macropore flow and ineffective irrigation, which can further provide practical guidance for scientific straw application.