Gust response analysis plays a very important role in large aircraft design. Most of existing aerodynamic models for gust response analysis are linearized models that can't be used for nonlinear aeroelastic analysis, such as transonic problems. In this paper, based on CFD technique and system identification method, a CFD-based reduced order model (ROM) is constructed in state space. It is compact and computationally efficient. Gust response analysis is completed by coupling structural equations with CFD-based ROM. A squareedged gust response for a typical wing is shown. The results of the responses of generalized displacements and root bending moment (RBM) are compared well with that of direct CFD method and the reference paper. It validates the correctness and precision of the CFD-based ROM method.