Agroecosystem functional assessment indicators provide a necessary bridge between decision-makers and scientists. The development of acceptable indicators, however, remains a difficult task because the current knowledge and understanding of ecosystems is not sufficient to allow an objective assessment of all ecosystem functions. These difficulties were summarized from three perspectives. First, there are difficulties in individual function assessment. Of the four functions associated with agroecosystems-energy flow, materials cycling, information flow and value flow - data on material cycling and information flow remain difficult to obtain and the indicators relatively immature. Secondly, there are difficulties of integration. During the assessment process, the integration of the agroecosystem functions remains the biggest obstacle. Until now, there has been no practical or effective methodology established to resolve the problem. At present, the makeshift approach has been to weight the various indicators and then add them together. Thirdly, there is the problem of obscure concepts and concept confusion. When assessments of agroecosystems are conducted, concepts such as structure, function, benefit, and resource utilization are used extensively. To date, no logical relationship(either real or implied) has been developed between any of these concepts. Are they causes and results such that the relationship between them is linear, or are they independent from one another such that the relationship is parallel? Thus far, the essence of this question is yet to be explored.