For two-axis electro-optical measurement equipment, there are many error sources in parts manufacturing, assembly, sensors, calibration, and so on, which cause some random errors in the final measurement results of the target. In order to eliminate the random measurement error as much as possible and improve the measurement accuracy, an active compensation technique for target measurement error is proposed in this paper. Firstly, the error formation mechanism and error transfer model establishment of the two-axis electro-optical measurement equipment were studied, and based on that, three error compensation and correction methods were proposed: the least square (LS)-based error compensation method, adaptive Kalman filter(AKF)-based error correction method, and radial basis function neural network (RBFNN)-based error compensation method. According to the theoretical analysis and numerical simulation comparison, the proposed RBFNN-based error compensation method was identified as the optimal error compensation method, which can approximate the random error space surface more precisely, so that a more accurate error compensation value can be obtained, and in order to improve the measurement accuracy with higher precision. Finally, the experimental results proved that the proposed active compensation technology was valid in engineering applicability and could efficiently enhance the measurement accuracy of the two-axis electro-optical measurement equipment.