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Soil amendments, such as straw mulch, organic fertilizers and superabsorbent polymer (SAP), are extensively applied to improve soil structure and porosity, and we reported the functional consequences of the individual application of these amendments in our previous study. However, whether combined amendments are more effective than their individual applications for improving soil pore structure is unknown. Here, we conducted X-ray computed tomography (CT) scanning on undisturbed soil columns to investigate the efficiency of two-amendment application, including straw mulch and organic manure, SAP and organic manure, or SAP and straw mulch, for improving soil pore properties and pore distribution. The X-ray CT technique allows us to accurately determine the number, morphology, and location of macropores (>1 mm in diameter) and smaller pores (0.13–1.0 mm). Compared to the control treatment, which showed the lowest increase in soil porosity, all the combined treatments led to an increase in the numbers of both macropores and smaller soil pores, causing a significant improvement in soil structure and porosity. Among these treatments, the application of both straw mulch and organic manure was the most effective for improving soil porosity and soil physical structure.