In order to clamp down on the illegal use of fishing boat fuel A (FBFA) and to reduce exhaust emissions in Taiwan, the residue from a desulfurization unit (RDS) and pyrolysis fuel oil (PFO) were added into FBFA with the ratio of 0.5% to form two new blended fuels (RDS0.5 and PFO0.5). The appearances of fuels from dark to light are RDS0.5, PFO0.5, and FBFA. The two new fuels have higher viscosity than FBFA, which may damage engines and reduce the misuse. The exhaust emissions of CO, HC, NOx, polycyclic aromatic hydrocarbons (PAHs), and carcinogenic potencies (BaPeq) were analyzed by the heavy duty diesel engine (HDDE) transient cycle test. The results show that RDS0.5 has significantly lower particulate matter (PM) emissions, while the PM emissions of PFO0.5 are higher than those of FBFA. In addition, the total PAHs emissions concentration of all three of fishing boat fuels increase from premium (regular) diesel fuel. However, RDS0.5 has relatively lower BaPeq emissions, which are usually considered as carcinogens, than the other fishing boat fuel.