This paper investigates the intelligent finite time formation control for multiple Flapping wing micro aerial vehicles (FWMAVs) system. Firstly, the translational and the rotational attitude motion equations are proposed based on the Lagrangian equation for FWMAVs. The motion system is decouple into an internal and an external dual loop subsystems. An adaptive neural network estimation algorithm is proposed based on the internal and external double loop system of the coupled model to effectively estimate the uncertainties and the external disturbances of the model. In addition, two effective intelligent control protocols are presented for the translational and the rotational attitude motion subsystem, respectively, by utilizing potential energy function, generalized inverse matrix, and finite-time stability. The main contribution of this paper is the case that, four control objectives are achieved for multiple FWMAVs system, including the estimation of uncertainties, collision avoidance, connectivity preservation, and finite time convergence. Finally, a simulation example of formation tracking control is given by using matlab software in the numerical simulation part, and the effectiveness of the obtained results and the superiority of the control protocol are verified.