An output-decision-based negative feedback control method and system. The method includes: receiving, by an output decider, output responses of at least two heterogeneous functional equivalents, and dividing numbers corresponding to the at least two heterogeneous functional equivalents into at least one set according to the output responses; determining, by the output decider, credibility of each set according to the output responses, and sending the at least one set and the credibility corresponding to each set to a feedback controller via decision information; generating, by the feedback controller, a first scheduling policy and/or a second scheduling policy according to the decision information; and sending, by the feedback controller, the first scheduling policy to an input proxy, and/or sending a change instruction to the heterogeneous functional equivalent indicated by the second scheduling policy. The method can prevent in advance and process a heterogeneous functional equivalent that may be faulty.