The present study is an attempt to examine the effect of biodiesel chemical structure on the diesel engine combustion properties and exhaust emissions. For this purpose, nine new types of oil (second generation) are used for producing biodiesel. Also, fatty acid profiles are determined by gas chromatography. Results show that Urtica biodiesel causes the highest soot emission (0.98 vol %) and the minimum NOx emission (460 ppm). A decrease in CN increases NOx and decreases soot emission at high engine loads. The longest chain is gained via Urtica biodiesel, and the increase of carbon chain length enhances soot emission. The increase of oxygen-to-carbon (O/C) ratio also affects the soot emissions and reduces the process (the O/C ratio is 0.1087 for Urtica). The increase of long-chain biodiesel fatty acids from C18 to C24 reduces the NOx emissions (C18−C24; 97.43 wt % for Urtica); moreover, there is a direct correlation between the increased carbon chain length and the amount of enthalpy. As the amount of unsaturated acids grows (94.93 wt % unsaturated fatty acids for Urtica), the value of the output soot is enhanced. Also, the increase in hydrogen-to-carbon ratio (1.8457 molar for Urtica) decreases the soot emissions. The increase in carbon chain length and decrease in O/C affect the HC and CO emissions; therefore, Urtica biodiesel had the maximum CO and HC emission (0.036 vol % and 6.11 ppm, respectively). In addition, the reduction of fuel consumption increased the NOx emission and reduced the HC, CO, and soot emission.