In the present study, we investigated the effects of concentrating a cell suspension of a hydrocarbon-rich microalga, Botryococcus braunii, by membrane filtration on hydrocarbon recovery efficiency. B. braunii suspensions before and after filtration were mechanically pretreated with a high-pressure homogenizer or a JET PASTER high-speed mixer. Concentrating the suspension increased the apparent viscosity of the sample and altered the particle size and shape distributions. The increase of viscosity was derived from the existence probability that was caused by shear forces in the pump that introduced the suspension into the membrane filter and/or between the membrane wall and algae. Homogenizer treatment decreased the sample viscosity from 20 to 5 mPa·s due to the collapse of the bridge between the algae and polysaccharides. The treatment also decreased the hydrocarbon recovery efficiency from 60% to 15% because of the release of intracellular substances that prevented hydrocarbon extraction. In contrast, JET PASTER treatment increased the hydrocarbon recovery efficiency by removing polysaccharides surrounding the colonies and disrupting colonies, without disrupting the cells. Adding oleic acid as a model intracellular substance to the concentrated sample before extraction decreased the amount of extracted hydrocarbon. These results demonstrate that concentrating the sample by filtration combined with JET PASTER treatment can improve the hydrocarbon recovery efficiency of B. braunii. In addition, an energy analysis was performed in the present study. The energy consumption of the JET PASTER treatment combined with filtration was 7.6 times as high as the energy produced.