Purpose This paper aims to solve the problems of baseline drift, susceptibility to abnormal data interference during baseline drift processing, and phase inconsistency in underwater acoustic target detection and signal processing of single microelectromechanical systems (MEMS) vector hydrophone. To this end, this paper proposes a baseline drift removal algorithm based on Huber regression model with B-spline interpolation (H-BS) and a phase compensation algorithm based on the Hilbert transform. Design/methodology/approach First, the Huber regression model is innovatively introduced into the conventional B-spline interpolation (B-spline) to solve the control point vectors more accurately and to improve the anti-interference ability of the abnormal data when the B-spline interpolation fitting removes baseline drift and the baseline drift components in the signals are fitted accurately and removed by the above method. Next, the Hilbert transform is applied to the three-channel output signals of the MEMS vector hydrophone to calculate the instantaneous phase and the phase compensation is performed on the vector X/Y signals with the scalar P signal as the reference. Findings Through simulation experiments, it is found that H-BS proposed in this paper has smaller processing error and better robustness than variational modal decomposition and B-spline, but the H-BS algorithm takes slightly longer than the B-spline. In the actual lake test experiments, the H-BS algorithm can effectively remove the baseline drift component in the original signal and restore the signal waveform, and after the Hilbert transform phase compensation, the direction of arrival estimation accuracy of the signal is improved by 1°∼2°, which realizes high-precision orientation to the acoustic source target. Originality/value In this paper, the Huber regression model is introduced into B-spline interpolation fitting for the first time and applied in the specialized field of hydroacoustic signal baseline drift removal. Meanwhile, the Hilbert transform is applied to phase compensation of hydroacoustic signals. After simulation and practical experiments, these two methods are verified to be effective in processing hydroacoustic signals and perform better than similar methods. This study provides a new research direction for the signal processing of MEMS vector hydrophone, which has important practical engineering application value.