The main purpose of this study is to analyze and compare the nano-particle emission characteristics by 3-different biodiesel blending rates in a CI engine. Nano-particle number density emitted from various operating conditions of compression ignition engine can be investigated by using the PPS (Pegasor Particle Sensor) system. Namely, some particle charged through the corona discharge in real-time can be measured by PPS system. Under the steady state operation of the 2.0L CRDi diesel engine with different operating condition and biodiesel blending rates, the nano-particle number density was analyzed at the downstream position of DOC system. As this research result, more engine load speed and higher the concentration of biodiesel blending rate showed that the nano-particle number density decreases. Also we found that DOC system for clean diesel engine is effectively useful instrument to reduce diesel particulate matter as resource of nano-particle generation.