The study analyzed the stability and reliability of the operation of the information system and adopted a control method that combines radial basis function and finite time stability theory. By constructing a control model based on radial basis function neural network and innovatively introducing a finite time tracking control framework, the framework can ensure that the system state reaches the desired system tracking performance in a limited time. In addition, a nonlinear mapping method is combined, and the control method is improved by integrating the backstepping method, which ultimately reduces the complexity and difficulty of information system design. Experimental tests have verified that under constrained conditions, the fluctuation amplitude of the corresponding curve of the intelligent information system is small, the speed of change is also slow, and the error of the state operation of the information system intelligent agent is also small. Practical application has proved that the proposed method can carry out good control of the system, and the tracking accuracy is high, which meets the needs of information engineering.