In order to improve the efficiency in computing the global properties of nonlinear systems, some effective methods have been proposed for the global analysis of these systems. However, there are only few investigations focusing on the numerical algorithms of the system response trajectories. This paper presents a higher-efficiency geometric numerical integration method with simple cell mapping for solving the basins of attraction of nonlinear systems. This numerical algorithm is based on the rule of Lie derivative, using it to calculate the trajectories of the nonlinear systems. Then, the global structure is studied by the numerical algorithm associated with a simple cell mapping method. Compared with the traditional Runge–Kutta methods of orders 4 and 5, it is demonstrated that the proposed Lie derivative iterative algorithm has significant advantages in efficiency.