Affected by high density, non-uniform, and unstructured seawater environment, fault detection of Marine Current Turbine (MCT) faces various fault features and strong interferences. To solve these problems, a harmonic analysis strategy based on zero-crossing estimation and Empirical Mode Decomposition (EMD) filter banks is proposed. First, the detection problems of rotor imbalance fault under strong interference conditions are described through an analysis of the fault mechanism and operation environment of MCT. Therefore, against various fault features, a zero-crossing estimation is proposed to calculate instantaneous frequency. Last, and in order to solve the problem that the frequency and amplitude of the operating parameters are partially or completely covered by interference, a band-pass filter based on EMD is used, together with a characteristic frequency selected by a Pearson correlation coefficient. This strategy can accurately detect the multiplicative faults under strong interference conditions, and can be applied to the MCT fault detection system. Theoretical and experimental results verify the effectiveness of the proposed strategy.