This work examines the control of nonlinear dynamic systems to synthesize a flight controller for Bat Bot (B2). B2 is a bat-inspired Micro Aerial Vehicle (MAV) which has articulated arm wings with several actuated and passive joints. B2 is designed to mimic the flight apparatus of actual biological bats, which is distinguished from other animals such as birds because bats employ numerous joints–more than 20 joint angles per each wing–and exhibit sophisticated motion patterns. B2 has significantly fewer degrees of freedom (DoF) than biological bats and the existing movements in the mechanism of B2 are: flapping motion of the wings, folding and unfolding of the wings and dorsoventral movements of the legs. The current work contributes to recent attempts to produce autonomous flapping flight motions in a bio-inspired robot with nontrivial morphology. This work uses the Lagrange framework to develop a nonlinear dynamic model for B2, and it proposes a nonlinear controller based on the theory of singular perturbation in order to track desired attitude angles.