The rapid and automatic acquisition of microscopic images of algae cells has important application value. To address the issues of sample injection efficiency and cell imaging quality in microfluidic-microscopic imaging technology, a method for detecting the average flow rate of samples based on the duration of algal cells passing through the fluorescence detection window is studied, and a segmented control method of microfluidic auto-injection based on volume flow regulation is proposed. The results show that the average flow rate detection error of the sample is less than 5% when the sampling speed is within the range of 10-30 μL/min, and the segmented control realizes the automatic acquisition of high-quality microscopic images for algae cells. The quality of the microscopic images is basically consistent with that of microscopy, while the sample injection speed is increased by more than 68%. The research results provide an effective and practical method for efficient and automatic acquisition of microscopic images of algae cells.