This paper presents Gaussian Process-based Feedback Linearization Control for quad-tiltrotor to compensate for aerodynamic uncertainty. Unlike the quadrotor platform, the quad-tiltrotor with wing shape is affected by aerodynamic force and moment, which cause unstable behavior in hover and transition modes. The proposed control scheme uses the Bayesian non-parametric method without prior knowledge to estimate the uncertainty with strong nonlinearity. First, we derive the mathematical modeling of the quad-tiltrotor, including an allocation matrix to consider the tilt-angle. Second, feedback linearization controller is designed by choosing desired target response model. Third, Gaussian process-based feedback linearization is proposed to enhance stable flight performance under situations of uncertainty. Lastly, numerical simulation is performed to compare proposed controller with feedback linearization with integral action.