In the process of pond culture, the usage of an aeration device can increase dissolved oxygen density and form a decent circulation which facilitates the collection of sludge. Acoustic Doppler Velocimeter (ADV) has been widely used to monitor the flow velocity, however, factors such as bubbles and suspended particles can affect the correlation coefficient and signal-to-noise ratio of ADV, which leads to the existence of outliers in velocity data. This study constructs the three-dimensional rousseeuw phase-space (3DRPS) method by optimizing the phase space threshold method and robust estimation method through two-step filtering and three-dimensional simultaneous measurement, where the outliers close to the real value can be detected more accurately and the iterative process can be reduced more effectively. The results show that the detection rate of the optimized 3DRPS method is approximately 99%. It is a promising method that effectively improves the accuracy of outlier detection and greatly reduces the phenomenon of over processing.