Abstract: Karst regions, characterized by widespread carbonate rock distribution and intense dissolution processes, develop a distinctive geochemical environment marked by high calcium content, alkaline conditions, low nutrient availability, and severe habitat fragmentation. Through three core mechanisms—direct chemical constraints (high Ca²⁺-driven ionic and acid–base stress), resource–energy constraints (low primary productivity and food scarcity), and structural–connectivity constraints (severe habitat fragmentation and spatial isolation)—this environment jointly shapes regional animal biodiversity patterns and adaptive evolutionary pathways across multiple spatial scales. This review summarizes the impacts of high-calcium stress, limited energy supply, and habitat isolation on animal morphology, physiology, behavior, and genetic differentiation, as well as the underlying adaptive mechanisms. In terms of physiological ion homeostasis, limestone langurs show blood calcium concentrations of 3.31 ± 0.27 mmol/L, significantly exceeding the normal physiological threshold in humans, indicating strong ion homeostasis regulation under high-calcium conditions. Regarding genetic differentiation, cave spider populations exhibit extremely high genetic differentiation (FST ＞ 0.9), indicating very limited gene flow and substantial population divergence driven by long-term spatial isolation. Regarding morphological and life-history adaptations, cavefish and arthropods generally exhibit eye regression, slow growth, and low reproductive rates, representing typical adaptive strategies in oligotrophic karst environments. In recent years, multi-scale testing and characterization techniques have provided important support for exploring habitat–biota coupling in karst systems. Existing studies have established integrated frameworks covering habitat structure, hydrogeochemical processes, and soil–sediment media, enabling cross-scale analyses of “habitat structure–material cycling–ecological response” and providing a quantitative basis for evaluating habitat suitability, resource availability and stability, and population connectivity. Karst animal biodiversity represents the integrated outcome of long-term interactions among geological, environmental, ecological, and biological factors. Compared with natural evolutionary processes, human activities have profoundly reshaped karst geochemical regimes at regional scales and become major drivers of biodiversity change in most disturbed habitats. Future studies should strengthen multi-scale and multi-factor coupling analyses, promote quantitative research on the linkage between geological–geochemical processes and animal ecological responses, and provide scientific support for karst biodiversity conservation and geo-ecological collaborative management.