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The integration of GPS compass, GPS differential technique and ADCP effectively eliminates the impact of magnetic interference and bottom tracking bias due to bedload movement, well improves the accuracy and widens the applications of ADCP measurement. However, an accompanying problem, the heading misalignment angle α between the ADCP's Y axis and external compass will be introduced into ADCP measurement and brings a significant impact on the calculation of flow velocity. Therefore it becomes very necessary to determine and compensate α. Although the conventional method, the Course Method, has been widely used in the determination of α, it still needs to be improved in the operability, efficiency, robustness, self-adapting detection and accuracy. Thus, a robust method, Multi-epoch Method, is proposed in this paper. In this method, with the help of GPS velocity and bottom-tracking velocity, a α can be got at each epoch, then a series of αs can be obtained at a course. Then, the final α can be achieved through filtering and averaging the series of αs. The new method efficiently overcomes the drawbacks of the conventional method, and can conveniently achieve an accurate α. A synthetic experiment has implemented to testify the new method. A α of 6.22° with internal-verification accuracy of ±0.04° and external-verification accuracy of ±0.04° is determined by the new method, which causes an absolute flow velocity error of −0.31~0.29m/s and a relative flow velocity error of nearly 56% in 4 transects, while after the correction of α, both of them decrease to less than 0.02m/s and 3.3% respectively, which are meet with the requirement of ADCP measurement. [ABSTRACT FROM AUTHOR]