This study was undertaken to document the causes of secondary deformities after surgery for correction of Wassel type IV-D thumb duplication. We carefully dissected and observed the flexor pollicis longus, and bone and joint anatomy in eight patients with secondary deformities after surgical correction. We transferred the flexor pollicis longus and thenar muscle attachments, reconstructed the A2 pulley, released and tightened the joint capsule, and performed osteotomies to correct skeletal malalignment. Kirschner wire fixation was used for 4–5 weeks, followed by brace fixation for 3 months. Patients were followed up for 13–34 months (mean 20 months). According to the Tada scores, the outcomes were good in six patients, and fair and poor in one patient each. The main causes of the secondary deformities were failure to reconstruct the A2 pulley, to transfer the flexor pollicis longus and thenar muscles, and incomplete resection of the radial metacarpal head. Brace fixation after Kirschner wire removal is crucial in preventing secondary deformities. Level of evidence: IV