In this paper, a mathematical model is developed for microalgae filtration by applying Population Balance Equation. The main objective is to investigate the impacts of cell size distribution and filter average pore size on filtration efficiency and their interrelationships. The results of using standard filters with different pore sizes are compared and discussed. Experiments of microalgae filtration on Chlorella cells are performed to provide size distribution information of the cell cultures to validate the model. Behaviours of cells at different sizes during the harvesting process are examined and the obtained data is combined with the mathematical model to evaluate the harvesting efficiency along with operation time and filter depth. The model could be extended to predict the size specific filtration efficiency of microalgae under different operation conditions, which potentially helps determine the process parameters for optimization purposes.