Soil pore structure affects microbial survival environmental conditions and thus enzyme activity. The mechanisms underlying returning organic materials on soil pore structure and enzymatic activity, however, remain unclear. We therefore conducted a field experiment in the fall of 2018 in northeastern China with a chernozem soil and four treatments: CT, conventional tillage; SCT, returning maize straw incorporation with conventional tillage; SIT, returning maize straw incorporation with inversion tillage; SMIT, returning maize straw and organic manure with inversion tillage. Soil samples were collected from the 0-15 cm and 15-35 cm layers in the fall of 2021. We used X-ray computed tomography to analyze the characteristics of pore structure and extracellular enzymatic stoichiometry to evaluate the limiting factors for soil microorganisms. Inversion tillage and organic materials incorporation can alter the micromorphological structure of entire soil layer, leading to the rearrangement of soil particles and nutrients, thereby augmenting the physicochemical properties in subsoil layer. SMIT exhibited a substantial increase in the number of macropores, porosity and fractal dimension, compared to SCT and SIT. This led to a significantly increased in soil enzyme activities of carbon and nitrogen-limited in SMIT, with increases ranging from 11.67% to 40.16% and from 8.81% to 21.43%, respectively (P < 0.05). Analysis using structural equation modeling revealed that returning organic material was conducive to the development of soil pore structure, characterized by an increase in macropores and fractal dimension and a decrease in the Euler number, had a positive correlation with soil enzyme activity. This, in turn, led to an alleviation in microbial nitrogen limitation. These results indicate that SMIT could serve as a viable choice in enhancing soil structure and fostering a favorable environment for microbial survival. Moreover, they offer essential insights into the microbial strategies responsible for the breakdown of organic matters in Hapli-Udic Cambisol.