Considering the superposition characteristics of the fuselage vibration of multi-rotor aircraft and the regulation effect of the phase between rotors on the overall vibration of the aircraft, a collaborative optimization calculation method for multi-target phase regulation vibration of multi-rotor aircraft was proposed. Firstly, a quadrotor/fuselage coupled vibration prediction model was constructed based on the Hamilton’s principle. By uniformly sampling and invoking the theoretical model to analyze the fuselage vibration response, the conflict of vibration response changes at two core parts, the flight control system and the camera mounting point position, under different rotor phase angles was revealed. Secondly, with the vibration of secondary nodes of the fuselage such as the connection between the support arm and the fuselage, the battery position, and the nose as constraints, the comprehensive optimization design of the flight control system and the camera mounting point positions was carried out by combining the dynamic Kriging surrogate model with the expected improved point addition and the NSGA-Ⅱ multi-objective genetic algorithm. Finally, the Pareto solution sets at stable level flight speeds of 18, 36, 54 and 72 km/h were generated. The trade-off relationship between the flight control system and the camera mounting point position under the phased vibration suppression strategy was revealed. Then, the minimum distance method was adopted to determine the final phase arrangement scheme. Compared with the 0° reference phase scheme, the vibration reduction efficiency of the camera mounting point position of the quadrotor unmanned aerial vehicle is 73.1%, 72.2%, 77.8%, and 67.1% respectively. The vibration damping efficiency at the positions of the flight control system is 75.3%, 74.3%, 76.9%, and 68.5% respectively. Moreover, the vibration damping efficiency can be further improved by adjusting the constraint threshold, ensuring that the multi-rotor aircraft can perform high-quality tasks in a good vibration environment. This proves the feasibility of the phased vibration theory of multi-rotors. It provides a brand-new approach and direction for the active vibration control design of multi-rotor aircraft.