Aiming at the low efficiency problem of the existing granulation reduction algorithms for multi-granulation rough set, an Effective Algorithm for Granulation Reduction of Multi-granulation Rough Set (EAGRMRS) was proposed. Firstly, the lower approximation Boolean matrix of decision classes was defined by using the decision information system as the object. The defined matrix could be used for converting redundant and repeated set operations into Boolean operations in the process of granular reduction. Based on this matrix, the algorithm for computing lower approximation of decision classes and the algorithm for computing the important measure of granularity were presented. Then, focusing on the problem of redundancy calculation when computing the important measure of granularity, a fast algorithm for computing the important measure of granularity with dynamic increasing of granularity was presented. On the basis, the EAGRMRS was proposed. The time complexity of the proposed algorithm is O(| A|·| U| ²+| A| ²·| U|), in which| A|is the size of granulation set,| U|is the number of instances in decision information system. The experimental results on UCI datasets show that, the proposed algorithm is effective and efficient, the efficiency advantage of EAGRMRS is more obvious over Heuristic Approach to Granular Structure Selection (HAGSS) for multi-granulation rough set when the dataset increases.