This study investigates the emission of a heavy-duty diesel engine generator fueled with waste cooking oil (WCO)-based biodiesel blends (W) and operated at 1.5 and 3.0 kW loads. A brand of pure fossil diesel was adopted as the base fuel, with 20% and 40% WCO-based biodiesel added into the based fuel to form W20 and W40 blends, respectively. The emission characteristics of PM, metals and PAHs were analyzed. Experimental results indicate that alternative WCO-based fuels had slightly higher fuel consumption rates (FCR) and brake specific fuel consumptions (BSFC) than conventional diesel (0.6–4.1% for FCR and 1.0–7.6% for BSFC), and similar engine thermal efficiency. The PM emissions reductions when using W20 and W40 were 19% and 6.5%, respectively, at 1.5 kW, and 27% and 19%, respectively, at 3.0 kW. The emissions of particle-bound metals were 13.6–13.8% lower when using W20 than using conventional diesel, but 12.0–12.3% higher when using W40. The metal contents of PM rose with the addition of WCO-based biodiesel. The metal elements of PM were dominated (> 90% mass) by Na, Mg, Al, K, Ca, Fe and Zn, while the major trace metals were Mn, Cu, Sr and Pb. The use of WCO-based biodiesel blends reduced the emissions of total-PAHs (44.0% in average) and total-BaPeq (80.2% in average). The mass reductions of MMW- and HMW-PAHs using W20 and W40 were more significant at 3.0 kW than at 1.5 kW, while the reduction of LMW-PAHs was greater at 1.5 kW than at 3.0 kW. Thus, the reduction in total-BaPeq was greater at the higher engine load. Accordingly, we conclude that the WCO-based biodiesel is a potential candidate of cleaner alternative energy sources.