Superconducting nanowire cryotrons (nTrons) are expected to be used as interfaces for super-high-performance hybrid devices in which superconductor and semiconductor circuits are combined. However, nTrons are still under development, and diverse analyses of these devices are needed. Accordingly, we have developed a numerical technique to simulate the three-terminal operation of an nTron by using the finite element method to solve the time-dependent Ginzburg–Landau (TDGL) equation and the heat-diffusion equation. Simulations using this technique offer understanding of the dynamics of the order parameter, the thermal behavior, and the characteristics of three-terminal operation, and the TDGL model reproduces qualitatively the results of nTron experiments conducted at the Massachusetts Institute of Technology. In addition, we investigated how some geometric and physical parameters (the design elements) affect the operation characteristics. The TDGL model has far fewer free parameters compared with the lumped-element electrothermal model commonly used for simulating superconducting devices. Furthermore, the TDGL model provides time-dependent visual information about the superconducting state and the normal state, thereby offering insights into the relationship between nTron geometry and three-terminal operation. These simulation results offer a route to nTron optimization and the development of nTron applications.