With the promotion of the laws about energy consumption of engines and the emission of pollutant in recent years, the technology of diesel engine is progressing. The use of High Pressure Common Rail, HPCR, is getting common. To protect the oil supply systems with high precision and smaller gaps, the fuel filters play a more important role. On the other hand, to reduce the use of fossil energy and the emission of greenhouse gas, every country is actively promoting the use of bio-fuel that can be regenerated. However, much research in the world all indicate that using biodiesel blend will cause problems to fuel filters, including lowering the emulsified water separation efficiency, shortening the usage life of fuel filters, and so on.Therefore, this research used the biodiesel made completely by the transesterification of waste cooking oil with different percentage of blend and the standard testing methods of ISO 19438 and ISO 16332 to study the effects on the filtration efficiency and fuel-water separation efficiency of the fuel filters. The testing results showed that with the increase of the percentage of biodiesel, the filtration efficiency of tiny particles of the filters increased slightly while the fuel-water separation efficiency decreased.