Flow cytomicrographic analysis is an important development in the automatic identification of planktonic algae in a water column, but the accuracy of this process is affected by the deformation of microscopic images under rapid injection conditions. Based on a microfluidic-microscopic imaging system for planktonic algae, the effects of flow rate on the deformation of microscopic images were investigated by analyzing the deformation of algal cells and image clarity at different injection flow rates. Based on the principle of deformation caused by photographing a moving object using a rolling shutter, a method of image deformation correction with unidirectional offset pixels is proposed and analyzed by comparing its results with images acquired under static conditions of algal cells. The experimental results showed that the average aspect ratio and sharpness of L values for oocystis cell images under static conditions were 1.16 and 116.53, respectively; during the dynamic injection process, the deformation (aspect ratio) of the cell images gradually increased and the sharpness decreased as the flow rate increased; the average values of aspect ratio before and after correction were 1.35 and 1.26 respectively at 95µL/min injection flow rate, and the dispersion of deformation decreased from 0.33 before correction to 0.1. The results are close to that of static cell morphology and the image sharpness is basically same. The results provide a method for improving the accuracy of the automatic identification of planktonic algal cells in a water column.