In this study, the time-varying wind stress drag coefficient in the Ekman model was inverted by the cubic spline interpolation scheme based on the adjoint method. Twin experiments were carried out to investigate the influences of several factors on inversion results, and the conclusions were (1) the inverted distributions with the cubic spline interpolation scheme were in good agreement with the prescribed distributions of the wind stress drag coefficients, and the cubic spline interpolation scheme was superior to direct inversion by the model scheme and Cressman interpolation scheme; (2) the cubic spline interpolation scheme was more advantageous than the Cressman interpolation scheme even if there is moderate noise in the observations. The cubic spline interpolation scheme was further validated in practical experiments where Ekman currents and wind speed derived from mooring data of ocean station Papa were assimilated. The results demonstrated that the variation of the time-varying wind stress drag coefficient with time was similar to that of wind speed with time, and a more accurate inversion result could be obtained by the cubic spline interpolation scheme employing appropriate independent points. Overall, this study provides a potential way for efficient estimation of time-varying wind stress drag coefficient.