Granular sludge is the basic unit of anaerobic granular systems, and the hydrodynamics of the sludge blanket is significantly governed by the granule characteristics. Although trapped bubble was one of the reasons to trigger granule floatation, until now, consensus has not been reached about the impact of bubble-entrapment on granule behavior and their spatial distribution in granular system. Besides, anaerobic granular sludge subjected to calcium-rich wastewater usually faced serious operational problems, leading to granule deactivation and sludge bed cementation. Bubble entrapment and calcium precipitation in granule change particle characteristics in opposite ways. In this study, a bubble entrapment model was proposed to infer the granule floatability based on the force balance between bubble-induced buoyancy and calcium precipitation-induced gravity. The results of the stratified sludge bed characterization conducted in two full-scale anaerobic reactors clearly present their diversified granule features in the vertical direction. The result shows that the lower boundary density for calcified granule was 1.10 × 103 kg/m3 and the most dynamic granules had a density ranged from 1.10 to 1.20 × 103 kg/m3. The comparative analysis of AnGS fluidization behavior and spatial distribution confirmed the reliability of the probabilistic prediction model of theoretical granule interception. Overall, these results contribute to an educated assumption into the understanding of the impact of granule density variation caused by biogas production and calcification on the formation of stratified sludge bed structure in anaerobic granular system.