For liquid fueled engine, the fuel atomization affects fuel’s evaporation, combustion, noise and vibration characteristics eventually. In this study, the effects of fuel species on the internal flow and near field primary breakup characteristics of a nozzle “Spray C” are investigated. Based on the framework of OpenFOAM, the newly developed solver which coupled cavitation model and the multifluid-quasi-VOF (Volume-of-Fluid) model, and combines the LES (Large Eddy Simulation) are applied to simulate the nozzle inner flow and near field jet breakup when using diesel and biodiesel respectively. The transient characteristics of nozzle inner flow and near field spray of two different fuels were analyzed, and the variation of axial pressure and velocity of nozzle was obtained. The simulation results show that the cavitation of biodiesel with high viscosity and low saturated vapor pressure develops slower and weaker. At the same time, due to the high viscosity of biodiesel, the flow velocity of the jet liquid column is slightly smaller than that of diesel, which makes the velocity difference between gas and liquid slightly smaller, and so is the drag force, resulting in the jet breakup penetration distance and turbulence disturbance that is not as strong as diesel. And the high density, viscosity and cetane number of biodiesel results in less vibration and noise compared to diesel.