This study aimed to compare the measuring stereopsis results of unilateral amblyopia during amblyopic treatment by employing some of the most widely used clinical tests. Thirty-four individuals with previously untreated unilateral amblyopia, aged 8.4 ± 2.7 years, were included in the study. Monocular (best corrected visual acuity [BCVA] at distance) and binocular (including Titmus, Random-dot, and Frisby stereopsis) visual functions were measured at baseline and 2-month and 6-month visits after synthetical treatment. We found that Titmus stereopsis was always significantly better than Random-dot stereopsis (p < 0.001). Frisby stereopsis was also always significantly better than Random-dot stereopsis (p < 0.001). However, there was no significant difference between Titmus stereopsis and Frisby stereopsis (p = 0.562). However, interestingly, there was no significant difference in the mean improvement of the three stereopsis methods from baseline to the 2-month visit, F = 1.158, p = 0.318. Similarly, a significant difference was also lacking in the mean improvement of the three stereopsis methods from baseline to the 6-month visit, F = 0.302, p = 0.740. We conclude that there will be different results obtained from different stereopsis measuring methods used to measure amblyopia in patients. We recommend performing at least two types of stereoscopic measurements to evaluate each case of amblyopia. However, for observing therapeutic effects, each measurement method has the same performance for clinical results during amblyopic treatment.