The invention discloses a multi-input photovoltaic inverter control method and system. In an independent connection mode, by obtaining difference between maximum power point directive voltage of each loop of photovoltaic module string and the actual PV voltage of the loop and obtaining the duty ratio of the loop through regulation, the control of a switching tube of each DC/DC circuit is realized and thus the control of the photovoltaic inverter is realized; in parallel connection mode, by obtaining difference between maximum power point directive voltage of a DC/DC circuit of a master loop and the actual PV voltage of the loop and obtaining the duty ratio of the master loop through regulation, the control of switching tubes of the master loop and the DC/DC circuits of each slave loop is realized and thus the control of the photovoltaic inverter is realized. By obtaining the duty ratio of multiple loops or one loop in the independent connection mode and the parallel connection mode, the scheme realizes the control of the photovoltaic inverter, the realization method is simple and reliable and the complex control of multiple loops of DC/DC circuits in the prior art is avoided.