The main goal of this study was to create a robust control system that could guide or replace the pilots in tracking of commanded velocity and attitude in multimodal maneuver, while complex dynamics and uncertain aerodynamic cross-coupling among control surfaces of compound helicopter are considered. To this end, a Pi-Sigma neural network (PSNN) adaptive controller is proposed based upon the certainty-equivalence (CE) principle, where a novel Lyapunov-based weight self-tuning algorithm augmented with e-modification is designed to realize efficient uncertainty approximation and guarantee robustness of convergence process. Compared with traditional neural networks in control field, stronger generalization ability of PSNN must be balanced against weaker stability, which leads to inevitable parameters perturbation. Therefore, an incremental nonlinear dynamic inversion (INDI) framework is established to decouple original overactuated system and reject parameters perturbation in PSNN. Meanwhile, by incorporating Lagrang- multiplier method into allocation, an original incremental allocation method is designed to get globally ideal control input according to time-varying working capability of each surface. In terms of Lyapunov theorem, it is demonstrated that the closed-loop augmented system driven by the proposed control scheme is semi-global uniformly ultimately bounded (SGUUB). Finally, the simulation result validates the effectiveness of proposed control scheme.