In this paper, a hybrid variational data assimilation scheme by extended control variable, which introduces flow-dependent background error covariance (statistically described with ensemble forecast perturbations), has been developed based on the CMA-TYM 3DVar system. Tests have shown that the assimilation of single-point typhoon central sea level pressure can cause the formation of asymmetric wind increments, and lead to the appearance of humidity increments that are considered irrelevant with pressure in the traditional 3DVar scheme. Experiments of a typhoon case show that the hybrid En3DVar scheme can effectively extract scattered observation data, and propagate it around according to the actual typhoon dynamic characteristics and distribution area, thereby it will change the structure and intensity of typhoon in the analysis field. At the same time, compared with the traditional 3DVar scheme, the hybrid En3DVar scheme has significant effect in improving the typhoon track and intensity forecast.