Purpose To further investigate the pathogenesis of late-onset capsular block syndrome (CBS) and to evaluate the safety of surgical treatment. Methods Seven patients diagnosed with late-onset CBS were retrospectively analyzed. Anterior chamber depth (ACD), intraocular pressure (IOP), refractive diopter, and best-corrected visual acuity (BCVA) before and after surgery were recorded. The opaque substance was tested with Western blot, and a flow cytometer multiple array assay system was utilized to evaluate the levels of inflammatory cytokines from opaque substance and aqueous humor, respectively. Results Patients who had undergone surgical treatment showed a significant BCVA and spherical equivalent refractive error improvement (P = 0.002, P = 0.021, resp.). Nevertheless, ACD and IOP before and after surgery were in normal range with no difference (P = 0.165, P = 0.749, resp.). αB-crystallin and βB-crystallin were detected in all opaque substances. Tumor necrosis factor-alpha (TNF-α) and interlukin-1β (IL-1β) levels in opaque substance were significantly higher than those in aqueous humor (P = 0.038, P = 0.007, resp.), while IL-2 and IL-6 were not detected in any samples. Conclusions Opaque substance is derived from human lens epithelial cells. Inflammatory cytokines may be involved in the pathogenesis of late-onset CBS. In addition, surgical treatment is an effective approach. This trial is registered with ChiCTR-IOR-17011287.