Abstract: Since the reform and opening-up was launched in 1978, environmental problems have increased due to unreasonable agricultural land use practices in China. Thus systematic analysis and evaluation of the environmental effects of agricultural land use, detailed understanding of material cycle mechanisms in agricultural systems and the improvement of material utilization efficiency have become a key research focus of land science. Substance flow analysis (SFA) is a systematic method of assessment of material flow and stock in a given system in the fabric of space and time. The SFA method is comprised of 3 parts — the sources, the pathways and the sinks. It characterizes the pathways of substances in, out and through a system and therefore an effective support tool for resources and environmental management. In this paper, an indicator system (including material input indicators, material output indicators, stock indicators, material intensity and efficiency indicators, and environmental health indicators) was established based on the SFA framework for the assessment of regional scale agricultural land use systems. The method was also used to assess material use efficiency and environmental quality in agricultural land use systems. Based on the cause-study analysis of Taojiang County (northern Hunan Province), material flow in the SFA framework in agricultural land use systems included productive input, production output, environmental output and stock. The results indicated that: (1) nitrogen derived from material productive input and environmental input sharply increased during the period from 1980 to 2013. The amounts of nitrogen derived from material productive input and environmental input in 2013 were respectively 1.2 and 0.4 times that in 1980. Productive input was the main source of nitrogen in Taojiang County. (2) Production output increased slowly during the period from 1980 to 2013. However, environmental output in 2013 approximatively doubled that in 1980. (3) There was an increasing trend in nitrogen material input intensity in Taojiang County during the period from 1980 to 2013. Material input intensity of nitrogen in 2013 was 328.4 kg?hm2, exceeding the critical value of 250.0 kg.hm^-2. In addition, material use efficiency of nitrogen decreased gradually during the period. Compared with the average value for Hunan Province, material production efficiency in agricultural land use systems in Taojiang County was lowest in 2013. It was therefore important for the local government to take measures to promote the adjustment process of agricultural structure and improve added value of agricultural products in the region. (4) The stability of the ecosystem and the quality of the environment reduced gradually for the period from 1980 to 2010, however, environmental quality improved during the period during 2010 to 2013. Nitrogen load decreased from 208.8 kg.hm^-2 in 2010 to 154.1 kg.hm^-2 in 2013. Although to a certain extent errors existed in the SFA analysis due to data shortage and difficulties in parameterization, the SFA method was a useful tool for the evaluation of material use efficiency and environmental quality in agricultural land use systems.