In traditional mathematical morphological filtering algorithm, the over-length of structure element has an adverse effect on filtering algorithm latency, hardware cost and other aspects. Due to the limitation, a modified mathematical morphological filtering algorithm with length-variable structure element is presented in this paper, which is modified by adding proportionality coefficient to the erosion and dilation algorithm. The mean filter is established on the new algorithm which is based on modified erosion and dilation operation. As a result, the precision of the modified mathematical morphological filter is guaranteed, meanwhile the length of the modified mathematical morphological filter is reduced sharply. Finally, the modified mathematical morphological filter is applied to the harmonic detection algorithm based on instantaneous reactive power theory. Simulation indicates that the modified filter has the performance of the low need of storage and rapid response.