Numerical analysis of a multibody mechanism moving in the air is a complicated problem in computational fluid dynamics (CFD). Analyzing the motion of a multibody mechanism in a commercial CFD software, i.e., ANSYS Fluent®, is a challenging issue. This is because the components of a mechanism have to be constrained next to each other during the movement in the air to have a reliable numerical aerodynamics simulation. However, such constraints cannot be numerically modeled in a commercial CFD software, and needs to be separately incorporated into models through the programming environment, such as user-defined functions (UDF). This study proposes a nonlinear-incremental dynamic CFD/multibody method to simulate constrained multibody mechanisms in the air using UDF of ANSYS Fluent®. To testify the accuracy of the proposed method, Newton–Euler dynamic equations for a two-link mechanism are solved using Matlab® ordinary differential equations (ODEs), and the numerical results for the constrained mechanisms are compared. The UDF results of ANSYS Fluent® shows good agreement with Matlab®, and can be applied to constrained multibody mechanisms moving in the air. The proposed UDF of ANSYS Fluent® calculates the aerodynamic forces of a flying multibody mechanism in the air for a low simulation cost than the constraint force equation (CFE) method. The results could have implications in designing and analyzing flying robots to help human rescue teams, and nonlinear dynamic analyses of the aerodynamic forces applying on a moving object in the air, such as airplanes, birds, flies, etc.