Abstract This paper analyzes the effect of clean energy use on total-factor efficiencies under the simultaneous consideration of economic output, energy conservation, and emission reduction. The empirical findings on 87 countries during 2004–2010 show that clean energy consumption significantly increases the total-factor emissions reduction efficiency (TFCE), slightly improves the total-factor economic output efficiency (TFYE), and significantly decreases the total-factor energy efficiency (TFEE), with the influence coefficients respectively 0.00292, 0.00029, and −0.00213. On balance, the comprehensive effect of clean energy consumption on total-factor technical efficiency (TFTE) is 0.00028. European countries have higher comprehensive efficiency in economic growth, energy conservation, and emissions reduction. International cooperation is needed to facilitate technology transfer and reduce the gap in efficiency.