Biogas engineering and the biogas-linked agricultural industries as a whole has been used as both a developmental strategy for rural new energy and an important part of renewable agriculture revolution in China. In this paper, we proposed a 3-level emergetic evaluation framework to investigate the energy efficiency and sustainability of a complex biogas system (CBS) in South China, comprising agro-industries such as planting, aquaculture, breeding and biogas. The framework is capable of tracking dynamical behaviors of the whole complex system (Level I), transformation processes (Level II) and resource components (Level III) simultaneously. Two new indicators, emergy contribution rate (ECR) and emergy supply efficiency (ESE) were developed to address the contribution and efficiency of resource components within each agro-industrial process. Our findings suggested the metabolism of the CBS were increased from 2000 to 2008, in which planting production was the biggest process in terms of total emergy input, while breeding was the most productive one with its highest total emergy yield. The CBS was under an industry transaction process stimulated by biogas construction, while the traditional agricultural activities still play an important role. For economic input, a trend towards a more renewable regime was found behind the total increase over time. With different preferences for renewable or non-renewable resources, planting and aquaculture production were proved natural donation-reliant, while breeding and biogas were economic input-dependent. Among all the economic inputs, electricity, diesels and infrastructure were the most efficient components in supplying all the processes. The challenges for the CBS rested in the relatively high transformities and the constant descent of sustainability within all processes. Armed with the 3-level emergetic framework, the status and dynamics of a complex system can be explicitly captured, making it possible to undertake a holistic yet microscopic optimization of biogas-linked production activities. (C) 2013 Elsevier Ltd. All rights reserved.