The Sinian Dengying Formation reservoirs in the Anyue Gas Field, Sichuan Basin, exhibit extreme heterogeneity. The existing karst geomorphological classification is too coarse to account for the significant differences in high-quality reservoir scale and productivity observed among adjacent wells within the same third- to fourth-order karst geomorphic units. To accurately predict the distribution of high-quality reservoirs, it is essential to reveal the precise mechanisms by which low-order micro-geomorphology controls paleokarstification and reservoir development. Based on 3D seismic data, core samples, thin sections, Formation MicroScanner (FMI) images, and geochemical analysis of data from the Gaoshiti–Moxi area, this study investigates how various micro-geomorphic units control karstification from both macroscopic and microscopic perspectives and subsequently analyzes their reservoir-controlling mechanisms. The results indicate the following: (1) The paleogeomorphology at the top of the Dengying Formation was restored using the impression method with a decompaction correction. A classification standard for micro-geomorphology at the top of the fourth member of the Dengying Formation (Z₂dn⁴) dolostone was established, identifying ten micro-geomorphic units, including coastal plains, river channels, and terraces. (2) Micro-geomorphic morphology dictates the distribution of the paleokarst hydrodynamic field, thereby controlling the intensity of karstification. River channels, terraces, and coastal plains, characterized by strong hydrodynamics, are the most favorable micro-geomorphic units. Inclined plains, with moderate hydrodynamics, are secondary favorable units. Conversely, concave plains and karst hills, with weak hydrodynamics and slow water alternation, are unfavorable units. (3) Six models of high-quality reservoir development, dominated by micro-geomorphic units in both intra-platform and platform-margin settings, were constructed, emphasizing the multi-element coupling of “strong karstification–40%–60% microfacies–faults”. This study reveals that micro-geomorphology is the key factor controlling the development of Z₂dn⁴ karst reservoirs. Predicting sweet spots by superimposing sedimentary facies and fault distributions onto micro-geomorphic maps can effectively improve the drilling success rate and development efficiency of deep carbonate reservoirs.