To avoid the difficulty of separating solids from liquids when reusing powder photocatalysts, 3D stereoscopic photocatalysts were constructed. In this study, three-dimensional S defect-rich MoS2 hierarchical aerogel was prepared by chemical cross-linking of functional ultrathin 2D MoS2. Its phase, micro-morphology and structure were characterized, and it was used in the study of photocatalytic degradation of organic pollutants. Of the samples tested, MS@CA-3 (i.e., defect-rich 3D MoS2 aerogel with a loading of 30 mg of defect-rich MoS2) exhibited the best photocatalytic activity due to its suitable load, good light transmission, and a degradation rate of up to 91.0% after 3 h. In addition, MS@CA-3 aerogel offers high recyclability and structural stability, and the degradation rate of the organic pollutant methylene blue decreases only 9.8% after more than ten cycles of photocatalytic degradation. It combines the high catalytic performance of S defect-rich 2D MoS2 and the convenient reusability of hierarchical porous aerogel. This study provides valuable data and a reference for the practical promotion and application of photocatalytic technology in the field of environmental remediation.