When the shipboard helicopter rotor engages and disengages on a ship deck, due to the influence of wind-over-deck environment and ship airwake, the heterogeneity of rotor airload is large. This large heterogeneity leads to the fluctuation of blade deflection which changes the aerodynamic forces and causes danger of over deflection. To investigate the aeroelasticity of a rotor blade and find the rule of deflection and the deformed blade aerodynamic force in the rotor/ship coupling flow field, we establish a loose computational fluid dynamics/computational structural dynamics (CFD/CSD) coupling model. This coupling model simulates the aeroelastic characteristics of the shipboard helicopter rotor during engagement and disengagement with ship motions. In the simulation, the CFD solver is based on Reynolds-averaged Navier-Stokes (RANS) equations and the CSD solver is based on the moderate deflection beam model. We compare the results with the experimental data and verify the effectiveness of the simulation. Through the analysis of the flow field, blade deflection, and aerodynamic forces under various wind-over-deck conditions at different positions, we find in certain cases, that the elastic deflection has a significant impaction the blade aerodynamic force. As the wind direction anglesincrease, the rotor blade is more likely to have a large negative elastic twist deflection, causing drop of aerodynamic forces and danger of over deflection.