A microphone-array-based speech recognition system combines a noise cancelling technique for cancelling noise of input speech signals from an array of microphones, according to at least an inputted threshold. The system receives noise-cancelled speech signals outputted by a noise masking module through at least a speech model and at least a filler model, then computes a confidence measure score with the at least a speech model and the at least a filler model for each threshold and each noise-cancelled speech signal, and adjusts the threshold to continue the noise cancelling for achieving a maximum confidence measure score, thereby outputting a speech recognition result related to the maximum confidence measure score.