The inner rotors of distributed propulsion tilt-wing Unmanned Aerial Vehicles (UAVs) are often folded in the cruising state and deployed in vertical take-off and landing to cope with the huge difference in thrust requirements. However, the blades of the conventional rotor have poor conformality with the nacelle profile, which will greatly increase the drag of the UAV after folding. This paper proposes an integrated method for the design of rotor and nacelle considering geometric compatibility to reduce the drag of the folded rotor and nacelle, so as to further improve the aerodynamic efficiency in cruise while ensuring the rotor efficiency in the vertical flight mode. A geometric mapping model based on nacelle design parameters and rotor design parameters is established, and a parametric model and aerodynamic optimization model of the outer arc airfoil family are developed. In addition, a rotor performance analysis model and a neural network response surface model for nacelle drag prediction that meet the requirements of confidence level are established. Based on the oblique inflow blade element momentum theory method, numerical simulation method, and genetic algorithm, an integrated optimization framework of the design of the conformal rotor and nacelle is built. Then, a geometrically compatible integrated optimization for the rotor and nacelle is carried out with the objective of maximizing energy efficiency in the full mission profile. Finally, a conformal rotor and nacelle design solution is obtained, which satisfies geometric compatibility and thrust constraints while providing high thrust efficiency and low cruising drag. A comparison of the results of the integrated design and the conventional rotor optimization design shows that the drag of the conventional rotor is 3.45 times that of the conformal integrated design in the cruising state, which proves the effectiveness and necessity of the proposed method.