A general method for geometric morphological analysis of complex blocks is presented by using the Boolean operations; and the corresponding program with C++ is developed. The Boolean operations are conducted with the Boolean intersection, union or difference operation of master and slave blocks to obtain more complex blocks. The concept of degenerate shell vector is introduced into the data structures of blocks to describe the finite discontinuities inside blocks; and then hybrid-dimensional models can be described in a block. The intersecting lines are obtained by conducting intersections between faces in master and slave blocks; and then the separated faces can be obtained by loop analysis. The effective and ineffective faces can be determined according to the specific Boolean operation. The new shells and blocks can be obtained by searching the effective faces. Four examples including one actual project are selected to validate the method. The results show that the proposed method can generate the more complex block and conveniently describe the finite discontinuities, showing that the method is universally applicable to the actual engineering.