Abstract: Emergy evaluation (EME) is an extensively used method for the assessment of ecological economic systems which has been applied in a diverse array of fields, with more recent application in agricultural systems. However, despite an increasing number of studies using the EME approach to assess agricultural systems, some of the evaluation principles of EME have been misunderstood by researchers applying the method resulting in unreliable assessments. Therefore, this study aimed to investigate issues identified from prior research using EME in the assessment of agricultural systems. Five common problems were identified: 1) disordered selection of unit emergy values (UEV) caused by updated global emergy baselines, 2) incomplete definition of system boundary, 3) arbitrary calculation of emergy contribution derived from environmental resources, 4) inoperable classification of system inputs, and 5) non-conservation between input and output emergy in agricultural systems. Concurrently, we proposed related solutions for resolving the identified problems which included: standardizing the selection principle of UEV in the EME; defining system boundary based on a standard of 'four-dimensional space-time scale'; constructing formulas to reasonably reflect energy contributions from soil and water for agricultural production in the EME; setting four standards to order the classification of input resources of agricultural systems; and applying the emergy accounting algebras to ensure the emergy conservation in research. We hope that our research will initiate further discussions on approaches to EME assessment in agricultural practices thus promoting a more standardized application of the emergy method in future studies.