Marine animal telemetry tags are carried by animals to collect environmental data and biological behavior data during their migration and dive. A micro hydropower system is proposed to power the telemetry tag, which can significantly increase its electrical energy. The hydropower is derived from the seawater head difference between the dive and surfacing of the tagged animal and is renewed by repeated dives of the animal. The mathematical model of the power system is built, and the test system for validating the mathematical model is built and tested. Based on the validated mathematic model, the analysis is conducted to obtain the performance and of the power system under single dive of tagged animals. The analysis results show that the power system can reach the energy conversion efficiency of 28.2% when the animal dives to depth of 600 m. The energy efficiency is influenced slightly by the dive depth of animals. When the power system is applied in telemetry tags, the electrical energy that it provide can outperform total energy of original battery of the same size in only several months. The micro hydropower system provides a novel and high efficient way in the ultra-high head hydropower generation.