Taking the Heihe river basin as a case study, this paper analyzes major critical ecological and economic problems. Further more, the system coupling theory is applied to propose a coordinated development mode of the Heihe river basin. The mode is divided into three levels: (1) agriculture coupling with the grass-livestock industry; (2) farm production coupling with the agriculture industry; (3) the eco-economic system of Heihe river basin coupling with other systems outside of the basin. At the same time, detailed approaches and methods of each coupling level are demonstrated as well in this paper.