Abstract Germanium-on-silicon (Ge-on-Si) single photon avalanche diodes (SPADs) have received wide attention in recent years due to their potential to be integrated with Si photonics. In this work, we propose and demonstrate a high-performance waveguide coupled Ge-on-Si separate-absorption-charge-multiplication SPAD with three electric terminals. By providing two separate voltage drops on the light absorption and multiplication regions, the drift and multiplication of carriers can be optimized separately. This indeed improves the freedom of voltage regulation for both areas. Moreover, thanks to the separate controlling, doping profile of the charge layer is greatly released compared to that of the conventional device because of the flexible carrier injection. In this scenario, the dark counts of the detector can be largely reduced through decreasing the electric field on the sidewalls of the Ge absorption region without affecting the detection efficiency. The proposed SPAD exhibits a high on-chip single photon detection efficiency of 34.62% and low dark count rates of 279 kHz at 1310 nm with the temperature of 78 K. The noise equivalent power is as low as 3.27 × 10−16 WHz−1/2, which is, to the best of our knowledge, the lowest of that of the reported waveguide coupled Ge-on-Si SPADs. This three-terminal SPAD enables high-yield fabrication and provides robust performance in operation, showing a wide application prospect in applications such as on-chip quantum communication and lidar.