In order to save time of sample processing and to improve the determining accuracy, a microwave-assisted extraction method was designed and optimized to extract chlorophyll-a in phytoplankton, and was compared to the freezing-thawing method for extraction efficiency of chlorophyll-a. The results showed that microwave-assisted extraction method was optimal in 60 s treatment with output power of 800 W, and the appropriate water volume for filtration was about 100-500 ml for samples collected in meso-eutrophic waterbodies and 1000 ml for those from oligotrophic waterbodies. The chlorophyll extraction rate of microwave-assisted extraction method was significantly higher than that of freezing-thawing method in meso-eutrophic waterbodies, which can increased by 7%-12%, while freezing-thawing method was more stable in measuring chlorophyll-a of oligotrophic waterbodies. For those algae with a glue shell or siliceous shell, microwave-assisted extraction method had a higher efficiency for chlorophyll-a extraction and a lower relative standard deviation than the freeze-thaw method. The microwave-assisted extraction method needs only one half operation time of the freezing-thawing extraction method, so that it is more suitable for emergency monitoring of eutrophic waterbodies, while the freezing-thawing extraction method is more suitable for monitoring oligotrophic waterbodies.