Since 2015, the coastal waters of Qinhuangdao have been experiencing bloomed of green tides from April to September, with Jinmenghaiwan bath being the main affected area. Previous studies have shown that micro-propagules play an important role in the formation of green tides. In this study, we aimed to assess the temporal and spatial distribution of green algae micro-propagules in the coastal waters of Qinhuangdao after the green tides bloom in 2020. We found that the number of green algae micro-propagules in Jinmenghaiwan bath was significantly higher than that of the other surveyed areas. In addition, these micro-propagules of green algae presented a distribution trend of “high near the shore and low away from the shore” pattern. Compared to the period from October 2016 to April 2017, both the number of green algae micro-propagules and the proportion of Ulva prolifera micro-propagules in the coastal waters of Jinmenghaiwan bath decreased considerably in the period from October 2020 to April 2021. This may also be the reason why the green tides scale in 2021 was significantly lower than that in 2017. The results of this study will provide a theoretical basis for early warning and control of green tides in Qinhuangdao.