Accurate and quantitative analysis of phytoplankton communities in lakes and rivers is very important to evaluate the health of lakes and rivers and ensure the safety of human drinking water. Microscopic examination is the only method for quantitative analysis of phytoplankton community structure, but it can not meet the requirement of phytoplankton count analysis. Based on the vision field method with an Utermöhl inverted counter, the method of using photograph taken by inverted microscope is put forward. This approach was used to count the three kinds of pure algae samples and Lake Poyang field samples and we found that: 1) The count is not accurate with the magnification of 5 or 10 times because the phytoplankton is too small, but accurate for 20 or 40 times. The number of photos is the main factor affecting the counting and analysis of the photo method, with higher accuracy for large numbers of photo-taken times. 2) For all the samples, the counting results are stable when taking 5 or 10 photos with magnifications of 20 or 40 times. 3) The method of inverted microscope photograph is more stable than that of counting frame, eyepiece field of view, and Utermöhl inverted counter field of view, with a minimum variation coefficient of 0.812.