This study examined the energy use, greenhouse gas (GHG) emission and the relationship between energy inputs and yield of cotton production in Iran. Data were collected randomly from 57 cotton farms using a face to face questionnaire. The results revealed the total energy of 31 237 MJ ha−1 which fertilizer, diesel fuel, and machinery were the main energy consuming inputs. Total GHG emission was 1195 kg CO2eq ha−1, and machinery, diesel fuel, and irrigation had the highest emissions. Energy ratio and energy productivity were 1.85 and 0.11 kg MJ−1, respectively. In order to explore the relationship between inputs and outputs, the Cobb-Douglas production function was applied and it was deduced that machinery, fertilizer, diesel fuel, and biocide energies had significant effect on cotton yield. Also, the results of marginal physical productivity technique indicated that an additional use of 1 MJ ha−1 from each of the biocide, machinery, and diesel fuel would lead to an increase in production by 1.68, 0.45, and 0.38 kg ha−1, respectively. The share of direct, indirect, renewable, and non-renewable energies was 40%, 60%, 29%, and 71%, respectively.