The present invention relates to a method for extracting lipids from microalgae using cationic polymers and a method for preparing biodiesel using the extracted lipids and, more specifically, to a method for extracting lipids from microalgae using polymers including positive charge groups and aliphatic chains in an end in order to destroy the cell wall of negatively charged microalgae without performing a drying process on the microalgae, and a method for preparing biodiesel using the extracted lipids. The method for extracting lipids from microalgae and the method for preparing biodiesel using the extracted lipids according to the present invention is able to reduce the energy of biodiesel and production costs since lipids is able to be extracted from microalgae without performing the drying process on the microalgae and is able to fulfill an environment-friendly biodiesel subprocess by interaction between the microalgae cell wall and polymeric coating without separate energy input and chemical substances consumed in a treatment process.