Modern agriculture heavily depends on energy consumption, especially fossil energy, but intensive energy input increases the production cost for producers and results in environmental pollution. Organic agricultural production is considered a more sustainable system, but there is lack of scientific research on the energy consumption between organic and conventional systems in China. The analysis and comparison of energy use between the two systems would help decision-makers to establish economic, effective and efficient agricultural production. Thus, the objectives of the present study are to analyze energy inputs, outputs, energy efficiency, and economic benefits between organic and conventional soybean (Glycine max (L.) Merrill) production. A total of 24 organic farmers and 24 conventional farmers in Jilin Province, China, were chosen for investigation in 2010 production year. Total energy input was 71.55 GJ ha–1 and total energy output was 96.18 GJ ha–1 in the organic system, resulting in an energy efficiency (output/input) of 1.34. Total energy input was 9.37 GJ ha–1 and total energy output was 113.4 GJ ha–1 in the conventional system, resulting in the energy efficiency of 12.1. The huge discrepancy in energy inputs and respective efficiencies lies in the several times higher nutrient inputs in the organic compared to the conventional production system. Finally, the production costs ha–1 were 33% higher, and the net income ha–1 25% lower in the organic compared to the conventional soybean production system. It is recommended to improve fertilizer management in organic production to improve its energetic and economic performance.