Biodiesel is a kind of clean and renewable fuel for diesel engine. The source of biodiesel affects the component and physicochemical properties of biodiesel, and it also influences the formation of particulate matter ( PM) during the combustion process. In this paper, the PM of diesel and 5 kinds of biodiesel from different sources were collected. In addition, the effects of biodiesel from different sources on morphology and PM diameter were analyzed. Taking the biodiesel made from waste cooking oil as the research object, the PM of diesel engine fueled with diesel/biodiesel blend ratio of 0%, 20%, 50%, 100% were collected by the test bench at engine speed 2000 r/min and engine torque 12.27 N.m. The effects of biodiesel on morphology, diameter, elements, functional groups and component of PM were analyzed. Results show that the average PM diameter of biodiesel from different sources is between 20 and 90 nm. The PM diameter of biodiesel made from cottonseed is larger than that from other different sources. From the test, the average PM diameter of diesel is 26.27 nm. With the increase of biodiesel blend mixing ratio from 0% to 20%, 50% to 100%, the diameter of PM is decreased by 7.9%, 17.2% and 24.2% compared with that of diesel respectively and the microscopic morphology of PM changes from ring to cluster. The analysis of X ray energy spectrometer shows that the content of C in PM is reduced. However, the content of O, Na, Cu, Al, Ba and Zn is increased. The analysis of X-ray absorption near edge structure shows that the content of "graphite" C = C, phenol C-OH, ketone C = O, aliphatic C = C in PM is decreased gradually, and the content of aliphatic hydrocarbon C-H and carboxyl C = O is increased. With the increase of biodiesel blend mixing ratio, the content of volatile organic compounds (VOF) is increased and the content of soot is decreased. When biodiesel mixing ratio reaches 50%, T-i, T-m, T-b and E of PM are decreased obviously from thermo-gravimetric analyzer test, it means that oxidation of PM was more actively.