Eye-in-hand robotic binocular sensor systems are indispensable equipment in the modern manufacturing industry. However, because of the intrinsic deficiencies of the binocular sensor, such as the circle of confusion and observed error, the accuracy of the calibration matrix between the binocular sensor and the robot end is likely to decline. These deficiencies cause low accuracy of the matrix calibrated by the traditional method. In order to address this, an improved calibration method for the eye-in-hand robotic vision system based on the binocular sensor is proposed. First, to improve the accuracy of data used for solving the calibration matrix, a circle of confusion rectification method is proposed, which rectifies the position of the pixel in images in order to make the detected geometric feature close to the real situation. Subsequently, a transformation error correction method with the strong geometric constraint of a standard multi-target reference calibrator is developed, which introduces the observed error to the calibration matrix updating model. Finally, the effectiveness of the proposed method is validated by a series of experiments. The results show that the distance error is reduced to 0.080 mm from 0.192 mm compared with the traditional calibration method. Moreover, the measurement accuracy of local reference points with updated calibration results from the field is superior to 0.056 mm.