It is a simple method to identify the hub dynamic loads of rotor by measuring the vibration responses on helicopter fuselage. However, the identification accuracy of the hub dynamic loads is related to the layout or placement of measuring points on the fuselage. The identification will be inaccurate if the layout of measuring points on the fuselage is unreasonable to result in the “ill-conditioned” frequency response function (FRF) matrix measured on the fuselage. In order to avoid the inaccurate identification due to the “ill-conditioned” measured FRF matrix, an accurate method for identifying the hub dynamic loads of rotor by vibration measurement on helicopter fuselage is proposed in this paper. In the proposed method, the reasonable layout of the measuring points on the fuselage for the “well-conditioned” measured FRF matrix can be obtained according to the condition number of the measured FRF matrix on the fuselage, and then the hub dynamic loads of rotor can be accurately identified. The simulation and experiment of the identification of the hub dynamic loads on a dynamically similar frame structure of a helicopter cockpit floor have verified the effectiveness and accuracy of the proposed method.