This paper presents an ecological analysis of agricultural systems in arid region of Northwestern China. Emergy analysis, a method for environmental accounting developed by H.T. Odum in the Eighties, is appropriate for this task because of its ability to transform different types of inputs to a common form (solar emergy) in order to allow scientific and objective comparisons across different period and regions. Taking Liangzhou and Minqin oases, located in the middle and lower reaches of the Shiyang River basin in Gansu province as a case study, the detailed structure of the agricultural process, input/output and emergy indicators of the systems are examined and compared for the years 1986 and 2000. Both the total emergy input and the total yield increased in the two oases. In Liangzhou Oasis the emergy of livestock production exceeded the traditional crop production, which still is the dominant production in Minqin Oasis. The emergy investment ratio, EIR, although increased in the investigated period, was less than 0.5 in both Liangzhou and Minqin oases, indicating that purchased materials and services were less than half the value of indigenous emergy sources exploited. As a consequence, the emergy yield ratio, EYR, was very high in both Liangzhou and Minqin oases. However, the increasing environmental loading ratio, ELR, and the decreasing environmental sustainability index, ESI, in the two oases illustrate a weakening sustainability of the two agro-ecosystems, and this tendency was more evident in the downstream Minqin Oasis, calling for more attention to the environmental degradation in the region.