The Tongwei-Weiyuan-Xiahe transect zone is located in the ecological zone of transition ranging form the Loess Plateau to the Qinghai-Tibet Plateau. It is a typical agri-pastoral transitional zone of the Northern China. For a long time, ecological and economic problems caused by the inappropriate agricultural production structure have severely restricted the sustainable development of grassland agriculture in this region. From the perspective of emergy, this research aims to (1) provide a new data support and theoretical basis for the adjustment of local agricultural production structure, policy formulation, and agricultural (pastoral) household decision-making in this area and (2) provide a scientific basis for the optimization of regional agricultural production structure. Input-output data of crop production and livestock production of households in the study area have been collected; the emergy value method has been adopted to analyze the input-output structure characteristics of crop production and livestock production, the production decision-making behavior of farmers, and the coupling effect of production systems. By applying the structural equation model (SEM), this research analyzed the energy conversion between components of production systems. It is demonstrated by this research that with the increase of altitude, crop production activities of farmers would decrease and the total output value of crops would also decrease. Although the main inputs and output factors of crop production are the same, the input emergy, output emergy, and emergy yield ratio of the same factor in different parts of the same crop can be varied. Significant differences can be seen from the input, output emergy value, and emergy yield ratio of the same factor at the same location of different crops (P < 0.05). In the input factors of crop production, the emergy value of organic fertilizer made significant contribution in Tongwei and Weiyuan. Agricultural production decision thresholds for crop input and output emergy values decreased from the east to the west, while the crop production scale in Xiahe expanded most rapidly when the initial input of emergy increased. Animal husbandry scale, emergy input, and output of animal production increased from the east to the west. In Tongwei and Weiyuan, wheat straw and alfalfa, as intermediate inputs, achieved 80% emergy contribution rate. In Xiahe, with animal production input factors, the contribution rate of supplement grain emergy value was as high as 90%, while the farm production decision threshold of livestock input and output emergy increased from the east to the west. The emergy yield ratio increased exponentially with the increase of the coupling degree. The speed of emergy yield ratio in both Tongwei and Weiyuan tended to decrease with the increase of the coupling degree, whereas, the speed of emergy yield ratio in Xiahe increased with the increase of the coupling degree. Adjusting the internal proportion of grain, cash crop, and feed products in crop production can strengthen the coupling effect between crop production and livestock production. Thus, optimizing the use of natural grassland and maximizing ecological benefits can be achieved. The threshold point can be used to regulate the production decision-making behavior of farmers and optimize the agricultural production structure in the region.