This paper addresses the unbalanced voltage, subharmonic/dc-offset voltage, and low-frequency (LF)/high-frequency (HF) harmonics of a grid voltage tracking method based on second-order generalized integrators (SOGIs) in high voltage/frequency swing on a shipboard photovoltaic (PV)-diesel-battery hybrid power system. To perform this work, a kind of shipboard PV⁻diesel-battery hybrid power system structure was first analyzed, emphasizing both the active and reactive power (PQ) control strategy and the sensitivity of the phase-locked loop (PLL) that is crucial to the vessel’s electrical networks. Then, the effect of grid voltage harmonics in SOGIs and of voltage/frequency swing on SOGI frequency-locked loop (SOGI-FLL) was studied. Meanwhile, aiming to the adverse power qualities of a shipboard power system (SPS), a SOGI-based structure with prefilter, a dc-offset block, and a positive sequence extractor (SOGI-FDE) was proposed. Finally, to overcome all of the vessel’s grid problems, a new SOGI-based voltage tracking structure, SOGI-FDE-FLL, consisting of SOGI-FDE and SOGI-FLL, was proposed to achieve accurate grid voltage tracking rapidly. This proposed schematic was used as an adaptive grid voltage tracking method to a three-phase three-wire shipboard PV⁻diesel-battery hybrid power system. Experimental results were obtained validating this proposal.