This research explores the influence of renewable fuels, including three kinds of biodiesel along with ethanol on the physical properties and structural characteristics of particulate matter (PM) emitted from a diesel engine in comparison with pure diesel. After adding 10 vol% of grape seed biodiesel, coffee biodiesel and eucalyptus oil into diesel, three biodiesel blended fuels (10% grape seed biodiesel (DGs10), 10% spent coffee ground biodiesel (DC10) and eucalyptus oil biodiesel (DEu10)) were produced and tested in this study. Besides, one ethanol blend containing 9 vol% of ethanol and 1 vol% of biodiesel (blend stabilizer) was also tested to do the comparison. In the present study, scanning transmission electron microscope (STEM) and scanning electron microscope (SEM) were employed for analyzing the microstructure, nanostructure and electron diffraction pattern of PM. Raman spectrometer (RS) was also used for the analysis of structural characterization of PM. In addition, several experimental instruments like microbalance, measuring cup, viscometer, oxygen bomb calorimeter and Gas Chromatography-Mass Spectrometer (GC-MS) were employed to detect the fuel properties, including density, heating value, viscosity, composition and cetane number. A conclusion can be drawn that both biodiesel blends and ethanol blend have a changing effect on the PM properties compared to pure diesel, where biodiesel blends have a slightly weaker influence than ethanol blend. Regarding the biodiesel blends, DGs10 has more impact than DC10 and DEu10 in changes of PM properties, particularly in the reduction of PM mass, making it a good candidate for renewable fuel for diesel engines.