The invention discloses a control system and method for a two-stage multifunctional grid connected converter. The control system comprises a front-stage control unit and a back-stage control unit, wherein the front-stage control unit is connected with a DC/DC converter and includes an MPPT controller; the back-stage control unit is connected with a DC/AC converter; the back-stage control unit includes a converter operating state detection module; the converter operating state detection module is used for acquiring an AC output current signal of the DC/AC converter and calculating the rate of change for the AC output current signal, and can obtain the operating state of a two-stage multifunctional grid connected converter by comparing the calculated rate of change with the preset rate of change threshold; an output signal of the converter operating state detection module is transmitted to a command current calculation module; the command current calculation module is used for receiving an output signal and a load current signal of the MPPT controller; and the output signal of the command current calculation module can form a back-stage pulse drive signal which drives the DC/AC converter to operate through modulation.