In order to sense the vortices generated by underwater moving bodies, a flexible bionic seal whisker sensor (Piezoelectric Seal Whisker Sensor, PSWS) based on piezoelectric nanogenerator is proposed. The design of the sensor is inspired by the biological structure of seal whiskers, while piezoelectric effect is utilized to obtain the sensing signal. Specifically, the sensor consists of a bionic whisker and a piezoelectric sensing unit encapsulated at its base, fabricated with polydimethylsiloxane (PDMS) and polyvinylidene fluoride (PVDF), respectively. Through series of towing experiments, the relationship between the output signals (voltage and frequency) of the PSWS and the perturbation/ vortex parameters (diameter of the spoiler column, distance between the PSWS and the spoiler column, and incoming flow velocity) was systematically investigated. The results show that the wavy geometry of the seal whiskers can suppress the vortex-excited vibration from the carrier’s motion, and there is certain relevance between the frequency and intensity of vortex shedding and the dimensions and distance of the disturbance column. This study exemplifies the potential of PSWS in acquiring the motion states of underwater bodies.