The invention discloses a harmonic reactive power compensation device as well as a control method thereof. The device comprises a bypass cabinet, an input transformer, a control device and a power cabinet, the input transformer adopts three-phase input, poly-phase winding output and the zigzag connection means, the power cabinet comprises 3N identical power units, input terminals of R, S and T at a rectifier side of each power unit are connected at output sides of the transformer, so each power unit has an independent direct current power supply, and the power units are mutually insulated and secondary windings of the transformer are also mutually insulated; wherein, N power units form one phase by means of cascade connection, all the power units are in star connection or in triangle connection with three phases correspondingly and then are connected with a power network by a reactor. The invention has advantages of high reliability, flexible control, realizable harmonic reactive power continuous compensation, fast response speed, high net side power factors and low total current harmonic wave.