The objective of this study was to investigate the performance and emissions of a diesel engine fueled by coal-based diesel fuels and their blends with oxygenated fuel polyoxymethylene dimethyl ethers (PODEn). First, coal-based Fischer–Tropsch diesel fuel was blended with hydrogenated diesel fuel at three volume ratios of 40%/60%, 50%/50%, and 60%/40%, denoted as T6W4, T5W5, and T4W6, respectively. Then, PODEn were added into the T4W6 fuel with the volume ratios of 10%, 20%, and 30% to evaluate its effects on the performance and emissions of a coal-based diesel engine. The results showed that the output torques and powers of the three coal-based diesel blends were slightly lower than those of the petroleum diesel fuel. The brake specific fuel consumption (BSFC) of the coal-based diesel fuels was almost the same as that of the petroleum diesel fuel. The brake thermal efficiencies (BTE) of the coal-based diesel blends were slightly lower than that of the petroleum diesel fuel, and the maximum reduction was 1.59%. The pollutant emissions of T5W5 were the closest to those of petroleum diesel fuel. The NOx emissions of T4W6 were lower, with a maximum decrease of 12.16% compared with the petroleum diesel. The carbon monoxide (CO) and hydrocarbon (HC) emissions of T6W4 were the highest, and the smoke emissions of T4W6 and T6W4 were higher than those of petroleum diesel fuel. Adding PODEn into T4W6 lowered the engine power and torque but increased the BSFC and BTE. The output torque and power of the diesel engine were further reduced when PODEn were blended with T4W6. With an increase in the PODEn blending ratio, BSFC and BTE increased gradually, and the maximum increase in the BTE was 1.57%. Blending PODEn with the fuel effectively improved the emission characteristics of the coal-based diesel fuels, and the NOx emissions increased slightly. The emissions of HC, CO, and smoke were reduced significantly, with maximum reductions of 19.15%, 26.65%, and 82.35%, respectively.