AIM: To evaluate the effect of femtosecond laser small incision lenticule extraction (SMILE) on the binocular visual function in myopic patients with glasses-free three-dimensional (3D) technique. METHODS: Totally 50 myopic patients (39 females and 11 males) with SMILE were enrolled in this prospective study. The glasses-free 3D technique was used to evaluate the binocular visual function in these subjects including static stereopsis, dynamic stereopsis, foveal suppression, and binocular balance point of signal to noise ratio (s/n ratio). All subjects received measurements in 1d before operation, and 1d, 1wk, and 1mo postoperatively. RESULTS: Both static and dynamic stereopsis showed no significant difference after SMILE. The foveal suppression improved significantly 1wk and 1mo after SMILE (P=0.005 and P=0.007 respectively). The binocular balance point of signal to noise ratio showed a significant improvement 1d, 1wk and 1mo after SMILE for both eyes (P<0.001 for each eye respectively). CONCLUSION: Glasses-free 3D technique can be used to evaluate the effect of SMILE on the binocular visual function in myopic patients perceptively, and SMILE can improve both foveal suppression and binocular imbalance in these patients.