In this paper, the transient probability density function and reliability function of generalized Van Der Pol stochastic system controlled by FOFOPID controller are studied. Firstly, the generalized harmonic function is introduced to transform the fast variable into the slow variable, and the new expression of FOFOPID controller in the form of slow variable is obtained by using the properties of fractional calculus. On this basis, because the radial basis function neural network has the advantages of high accuracy, easy to solve highdimensional problems, fast solving speed and so on, we apply the radial basis function neural network to solve the forward and backward Kolmogorov equations satisfied by the stochastic system respectively, and obtain the transient probability density function and reliability function. Finally, by analyzing the influence of fractional calculus in the controller on the response and reliability of Van Der Pol stochastic system, we come to the conclusion that fractional order controller will enhance the response of the system to a certain extent and lead to bifurcation.