A multiphysics-coupled numerical simulation of a segmental annular thermoelectric cooler (SATEC) was performed using a three-dimensional finite element method. A coupling model of the temperature, stress, and electric fields was established based on the three-dimensional transient states. Moreover, the effects of different pulse width (τ), pulse current amplitude (Pa), pulse current shape parameter (m), heat transfer coefficient (h), angle (θ), and length (H) of the thermoelectric leg on the SATEC transient properties and von Mises stress were studied. The results show that τ and Pa are the key influencing factors of SATEC. The larger the h, the more optimized the heat transfer effect of the SATEC hot end. However, when h increased to a certain value, the changes in the transient performance were insignificant. The optimal pulse can be achieved when the input pulse current Iop = 6.47 A and pulse width τ = 20 s. When the length of the thermoelectric leg H4 was 3 mm and the thermoelectric leg angle θ2 was 7°, the performance of SATEC was optimal, with Tc,min being 249.57 K, Tc,max being 279.50 K, thold being 5.5 s, and the maximum von Mises stress being 37.48 MPa. The results show that different supercooling indices and von Mises stresses could be obtained for different pulse current shapes. Geometric optimization of SATEC can improve the cooling performance and reduce the von Mises stress, thereby providing a theoretical reference for practical engineering applications and thermoelectric cooling research.