Estimation of the production function is among the techniques applied to gain knowledge on the production sustainability status of agricultural systems. However, variations in the units of crop measurement and of the inputs to the model function used for estimation are considered as drawbacks, when investigating the stability of ecosystems. The present research is to calculate all inputs and outputs of the econometric model using the emergy technique, which expresses all terms in the model in the same unit, solar emjoules. It is important to bring up free environmental inputs in the production function and consider them as economic inputs affecting sustainability. Align the unit of measurement of all inputs and outputs, estimation of the input production function in uniform and powerful unit of solar emjouls (sej), considering free energy of solar radiation and the amount of soil organic matter and minerals indicates the comprehensiveness of the method compared to conventional production estimation methods. In this study, the sustainabilities of mechanized and traditional rapeseed production systems were compared with parameters derived from the estimation of the production function in Lorestan, Iran. Data were collected through questionnaires and continuous communication with 40 producers of rapeseed by mechanized methods (i.e., the producers using the highest level of mechanization) and 40 traditional rapeseed farmers (i.e., the producers using the lowest level of mechanization) among a total sample of 1489 rapeseed farmers active in 2018. Results showed elasticity values for soil organic matter reduction and erosion input in mechanized systems was −1.58 and for water, workforce, nitrogen and phosphorous fertilizers, and chemical pesticide inputs in traditional systems were −1.31, −3.53, −0.36, −2.30 and −1.51, respectively. These negative elasticities suggest that sustainability is threatened due to the excess consumption of these inputs. Application of policies to 1) integrate small land holdings into the total production function for rapeseed, 2) increase the knowledge and skills of the workforce in the agricultural sector, and 3) implement conservation measures to prevent soil organic matter reduction and erosion are practical approaches are suggested to improve the productivity and sustainability of these agricultural systems.