Background Nanophthalmos is a rare congenital ocular disorder characterized by a short axial length (AL), which predisposes to secondary angle-closure and secondary angle-closure glaucoma. Surgical management is challenging due to high complication risks. This study aimed to evaluate the  feasibility and efficacy of phacoemulsification with intraocular lens implantation and goniosynechialysis (Phaco+IOL+GSL) in nanophthalmos with secondary angle-closure or secondary angle-closure glaucoma, and to propose a stepwise complication management strategy. Methods This retrospective case series included 20 eyes of 20 patients diagnosed with nanophthalmos (AL < 20 mm) and PAC (2 eyes) or ACG (18 eyes) who underwent Phaco+IOL+GSL between January 2022 and Jun 2025. Patients were divided into three groups based on AL: Group A (14 mm ≤ AL < 16 mm, 9 eyes), Group B (16 mm ≤ AL < 18 mm, 4 eyes), and Group C (18 mm ≤ AL < 20 mm, 7 eyes). Preoperative and postoperative uncorrected visual acuity (UCVA, logMAR) and best-corrected visual acuity (BCVA, logMAR) were recorded, intraocular pressure (IOP), number of antiglaucoma medications, and intraoperative and postoperative complications were analyzed. Results At the final follow-up (6-12 months postoperatively), the median IOP significantly decreased from 25.5 [16.0, 35.0] mmHg to 16.0 [14.0, 19.0] mmHg (P < 0.05). The median number of antiglaucoma medications decreased from 2.5 [0.0, 4.0] to 0.0 [0.0, 0.0] (P < 0.05). UCVA improved from 1.30 [1.00, 1.70] to 0.40 [0.12, 1.10] (P < 0.05), and BCVA improved from 0.82 [0.40, 1.30] to 0.70 [0.30, 1.30] (P = 0.035). The qualified success rate was 95.0% (19/20), and the complete success rate was 80.0% (16/20). The intraoperative complication rate was 25.0% (5/20), primarily shallow anterior chamber. The postoperative complication rate was 40.0% (8/20), primarily shallow anterior chamber with elevated IOP. Complications were concentrated in Groups A and B. Multivariate logistic regression analysis revealed that shorter AL was significantly associated with a higher risk of surgical complications (OR = 0.439, P < 0.05). A stepwise management strategy—initiating with medical/laser therapy, escalating to cyclophotocoagulation, and reserving pars plana vitrectomy for refractory cases—achieved successful complication management. Conclusion Phaco+IOL+GSL is a feasible and effective procedure for nanophthalmos with secondary angle-closure glaucoma, reducing IOP, medication dependence, and improving visual acuity. Compared with more complex combined procedures(e.g., with prophylactic vitrectomy or sclerectomy) , this technique is simpler and less invasive. A stepwise management strategy effectively addresses complications. Shorter AL, particularly <16 mm, is associated with higher surgical risk.