The invention relates to a new energy grid-connected operation control method and system. The method includes the following steps that: an active distribution network is partitioned; a fault region isidentified through the fault direction information of each region, and the operation mode of each region is controlled according to the position of the fault region, wherein the fault direction information contains a fault current direction and a power flow direction identifier. With the new energy grid-connected operation control method and system provided by the technical schemes of the invention adopted, partitioned control can be performed on the malfunctioned active power distribution network; a distributed power source can continue to supply power to regions in isolated island operation; the power outage range of the distribution network is reduced; the potential of the distributed power source is fully utilized; and the reliability of power supply is improved.