It is a challenge to improve the accuracy of 3D profile measurement based on binary coded structured light for complex surfaces. A new method of weighted fusion with multi-system is presented to reduce the measurement errors due to the stripe grayscale asymmetry, which is based on the analysis of stripe center deviation related to surface normal and the directions of incident and reflected rays. First, the stripe center deviation model is established according to the geometric relationship between the stripe center deviation, the incident and reflected angles at any measured point. The influence of each variable on stripe center deviation is analyzed, and three subsystems are formed by a binocular structured light framework to achieve multiple measurements based on the influence regularity. Then in order to improve the measurement accuracy, different weights are assigned to the measured point in different subsystems according to the stripe center deviation model and its relationship with measurement error, and the weighted data from different subsystems are fused. Experiments are carried out to validate the presented method, and the experimental results demonstrate that it effectively improves the measurement accuracy of complex surfaces and measurement accuracy is improved by about 27% compared with the conventional method.