Purpose: When a manipulator captures an unknown space object, inertia parameters of endpoint payload should be timely obtained to handle possible unexpected parameter variations and monitor the system’s operating conditions. Therefore, this study aims to present an identification method for estimating the inertia parameter of the payload carried by a flexible two-link space manipulator. Design/methodology/approach: The original nonlinear dynamics model of the manipulator is linearized at a selected working point. Subsequently, the system modal frequencies with and without payload are determined using the subspace identification algorithm, and the difference of these frequencies is computed. Furthermore, by adjusting the structural configuration of the manipulator, multiple sets of frequency differences are obtained. Therefore, the inertia parameters of the payload, i.e. the mass and the moment of inertia, can be derived from the frequency differences by solving a least-squares problem. Findings: The proposed method can effectively estimate the payload parameters and has satisfactory identification accuracy. Practical implications: The approach’s implementation provides a practical reference for determining inertia parameters of an unknown space target in the capture process. Originality/value: The study proposes a novel method for identifying the inertia parameters of the payload of a flexible two-link space manipulator using the estimated system frequencies.