On the basis of the present research progress of ecological agriculture, we take Minle County and Linze County located in the middle reaches of Heihe River as the typical research units. Based on the rural social and economic data during the period of 2000-2010, theory and method of mathematical statistics are used to establish the measure theory and model of agro-eco-economic system harmony coefficient, including efficacy function, function of harmony coefficient, harmony coefficient and level of harmony coefficient. Based on the actual situation of research region, evaluation indicator system of agro-eco-economic system is established and measurement is carried out. Results show that the regional agro-eco-economic system in research region was in a serious imbalance in 2000-2013. The harmony coefficient of Minle showed a slight rise from 2000 to 2004, and then presented a fluctuating decline. Its rank of harmony coefficient experienced serious imbalance-extreme imbalance-moderate imbalance-low imbalance-serious imbalance-high imbalance. At the same time, the similar tendency happened in Linze County. The measuring results of subsystem in 2000-2013 further indicated that except that the harmony coefficient of economic subsystem in Minle County and Linze County was moderate and high, the ecological subsystem was at Level II and Level III, and social subsystem was at Level IV and Level III, in high and low imbalance status. Finally, several recommendations were put forward for optimizing agro-eco-economic system.