The piezoelectric vibration energy harvester (PVEH) based on the variable cross-section cantilever beam (VCSCB) structure has the advantages of uniform axial strain distribution and high output power density, so it has become a research hotspot of the PVEH. However, its electromechanical model needs to be further studied. In this paper, the bidirectional coupled distributed parameter electromechanical model of the MEMS VCSCB based PVEH is constructed, analytically solved, and verified, which laid an important theoretical foundation for structural design and optimization, performance improvement, and output prediction of the PVEH. Based on the constructed model, the output performances of five kinds of VCSCB based PVEHs with different cross-sectional shapes were compared and analyzed. The results show that the PVEH with the concave quadratic beam shape has the best output due to the uniform surface stress distribution. Additionally, the influence of the main structural parameters of the MEMS trapezoidal cantilever beam (TCB) based PVEH on the output performance of the device is theoretically analyzed. Finally, a prototype of the Aluminum Nitride (AlN) TCB based PVEH is designed and developed. The peak open-circuit voltage and normalized power density of the device can reach 5.64 V and 742 μW/cm3/g2, which is in good agreement with the theoretical model value. The prototype has wide application prospects in the power supply of the wireless sensor network node such as the structural health monitoring system and the Internet of Things.