Abstract: The prerequisite for an agricultural ecosystem that wants to be run benignly is its structural diversity, while the major dynamics is the structural dominance.This paper dealt with the running mechanism of agricultural eco engineering (A EE) by analyzing the structure of a typical AEE model in Xishan village, Shandong P rovince. The harmony between structural diversity and dominance is considered as one key issue for good function of an agroecosystem. The important reason that the agroecosystems in Xishan village have developed sustainably in a long term, w ith a tendency of slowing down its speed recently, is the harmony between struct ural diversity and dominance. The structural diversity index has kept in a high level for a long time with the highest 0.6556, and harmony among components in d ifferent structural chains is all over 90%. Meanwhile, the dominance index has k ept in a low level with highest 0.2574, and the highest harmony index is only 0. 1327. It is suggested that the system structure harmony should be maintained in order to guarantee the sustainable development of AEE.