The harmony monitoring mechanism of government system is put forward for improving the synergetic effect and harmony of the government system and to construct the one-stop high-synergetic services-oriented government. The direct disharmony matrix and total disharmony matrix of each element of the government system can be calculated through the concept of disharmony. And the disharmony degree, restricted degree and total disharmony degree of each element can be calculated through the two matrixes. The D-C space distribution structure map which describing the controllable degree and harmony of each element also can be generated in this method. The implementing of the harmony monitoring mechanism will be demonstrated in a data analyze case. This monitoring mechanism can help the government system to discovery the disharmony factors in the department and to improve the elements that located in the disharmony district. Also this mechanism offers the decision support to the high-synergetic services-oriented government.