Geological exploration cores obtained from shale gas wells several kilometers deep often show different height-diameter ratios (H/D) because of complex geological conditions (core disking or developed fractures), which makes further standard specimen preparation for mechanical evaluation of reservoirs difficult. In multi-cluster hydraulic fracturing, shale reservoirs between planes of hydraulic fractures with different lengths could be simplified to have different H/D ratios. Discovering the effect of H/D on the mechanical characteristics of shale specimens with different bedding orientations will support mechanical evaluation tests of reservoirs based on disked geological cores and help to optimize multi-cluster fracturing programs. In this study, we performed uniaxial compression tests and acoustic emission (AE) monitoring on cylindrical Longmaxi shale specimens under five bedding orientations and four H/D ratios. The experimental results showed that both the H/D-dependent mechanical properties and AE parameters demonstrated significant anisotropy. Increasing H/D did not change the uniaxial compressive strength (UCS) evolution versus bedding orientation, demonstrating a V-shaped relationship, but enhanced the curve shape. The stress level of crack damage for the specimens significantly increased with increasing H/D, excluding the specimens with a bedding orientation of 0°. With increasing H/D, the cumulative AE counts of the specimens with each bedding orientation tended to exhibit a stepped jump against the loading time. The proportion of low-average-frequency AE signals (below 100 kHz) in specimens with bedding orientations of 45° and 60° increased to over 70% by increasing H/D, but it only increased to 40% in specimens with bedding orientations of 0°, 30°, and 90°. Finally, an empirical model that can reveal the effect of H/D on anisotropic UCS of shale reservoir was proposed, the anisotropic proportion of tensile and shear failure cracks in specimens under four H/D ratios was classified based on the AE data, and the effect of H/D on the anisotropic crack growth of specimens was discussed.