Accumulated carbohydrate in microalgae is promising feedstock for bioethanol fermentation. Selection of suitable cultivation conditions in semi-continuous cultivation is critical to achieve a high carbohydrate productivity. In the current study, the effects of macro-nutrient (nitrogen, phosphorus, and sulfur) limitations and light intensity were evaluated for the carbohydrate accumulations of Chlorella sp. AE10 under 10% CO2 conditions. It was shown that nitrogen limitation and high light intensity were effective for improving carbohydrate productivity. The average carbohydrate and biomass productivity in semi-continuous cultivation with 1/4 N medium and 1000 mu mol photons m(-2) s(-1) was 0.673 and 0.93 g L-1 day(-1), respectively. Sulfur and phosphorus limitations could improve the carbohydrate content but they could not enhance the carbohydrate productivity. The cell cycle progression and chlorophyll a were investigated using flow cytometry (FCM). The results showed that macro-nutrient limitation and high light intensity indeed influenced cell cycle progression and led to the formation of polyploid cells along with the carbohydrate accumulation in a certain range. FCM was rapid and accurate method to investigate the operation conditions why 1/4 N, 2 days as a cycle, and high light intensity were optimal ones. In addition, the remaining high level of photosynthesis activity was also important for achieving a high carbohydrate productivity. Dynamic tracking of carbohydrate accumulation is helpful for establishment of a semi-continuous cultivation for enhancing carbohydrate productivity in microalgae.