A vehicle able to navigate both in the air and underwater is referred to an unmanned aerialunderwater vehicle (UAUV). In this paper, the attitude and altitude control of UAUV with a quadrotor configuration during underwater navigation is studied theoretically, and an incremental dynamic inverse control (INDI) method with second-order low-pass filters is employed in the control system. Based on the underwater motion model of an UAUV and the incremental attitude and altitude control model, the relationship between thrust increment and vertical and angular acceleration increment is obtained through Taylor series expansion and angular acceleration feedback. Subsequently, attitude and altitude controllers based on nonlinear dynamic inversion (NDI) and INDI are designed and their robustness is analyzed. By introducing second-order low-pass filters at the part of control and feedback, the accuracy of the angular acceleration estimation is improved and the time synchronization of the control system is ensured. Simulation results demonstrated that when introducing external disturbances and uncertainties, the INDI control with second-order low-pass filters proposed in this paper can track the reference signal faster and more accurately than the NDI control. INDEX TERMS Unmanned aerial-underwater vehicle (UAUV), incremental nonlinear dynamic inversion (INDI), attitude control, nonlinear dynamics, low-pass filter