Passive binocular measurement systems are being increasingly utilized in the in-situ industries of automobiles, aviation, and aerospace, etc. due to their excellent qualities of accuracy, efficiency, and cost performance. Whereas the barrier of evaluating the accuracy of measured objects resulted from the unequal equivalent focal length and quantization of pixels, has limited their further development and application of high requirements for in-situ machining, e.g., the measurement of machining reference points for the positioning of robotic drilling in aerospace manufacturing. In this paper, an accuracy evaluation method is proposed to address the problem. Firstly, the unequal equivalent focal length is considered to improve the accuracy of 3D reconstruction. Next, the credibility probability model is developed to calculate the probability of the observed error in the public view of the binocular measurement system and indicates the direction of improvement. Finally, the in-situ experiment is carried out to validate the method within the effective public view range of 300 mm × 300 mm. The experiment results show that the RMSs of observed errors are superior to 0.035 mm, and the credibility probabilities are all higher than 0.91; the maximum 3D reconstruction accuracy improvement is 60.3%, with the error reduced from 0.078 mm to 0.031 mm.