Micro/nano-electrical discharge machining is an alternative preparation method for surface micro/nano-structures, but it is difficult to precisely control the size of the micro/nano-structures due to its unclear material removal mechanism. Thus, it is useful to study its machining mechanism to achieve high-efficiency and controlled processing. At present, most of the established EDM thermal models for predicting the discharge crater size are based on the classical Fourier heat conduction law, assuming that the conduction velocity of heat energy is infinite. However, the single-pulse discharge time of micro/nano-EDM is transitory (<1 μs), and thus, the steady state heat balance condition cannot be achieved in a single-pulse discharge time. In order to predict the size of the micro/nano electrical discharge craters more accurately, the non-Fourier effect was considered to study the temperature field distribution of micro/nano-EDM of single-pulse discharge machining. Firstly, the classical Fourier heat conduction law was modified by introducing a relaxation time. Secondly, several key factors were considered to establish the thermal model of micro/nano-EDM in single-pulse discharge machining. Subsequently, numerical simulation software was used to solve the thermal model for obtaining the temperature field distribution of the workpiece material and predicting the size of the discharge craters. Finally, the predicting accuracy of the new thermal model was evaluated by comparing the relative error between the simulated values and experimental values. The comparison results show that considering the non-Fourier effect can reduce the average error of the thermal model from 33% to 10%. The non-Fourier effect is more obvious under the shorter discharge time of a single pulse.