In situ growth rate of five algae species with different C-S-R growth strategies and the main influencing factors under different operating stages of the Three Gorges Reservoir were investigated by applying the field incubation experiment in semi-enclosed cove at Lake Gaoyang of the Pengxi River. The results showed that Cyclotella hubeiana(with CR growth strategy) and Cryptomonas ovata(with CRS growth strategy) displayed the positive growth rates which were 0.128 ±0.006 and 0.210 ±0.010 d^-1, respectively. Both of them were the dominant algae in the lake during low water level stage. Cyclotella hubeiana, Eudorina sp. (with CS growth strategy) and Cryptomonas ovata had higher growth rates which were 0.175 ±0.009, 0.326 ±0.016 and 0.187 ±0.009 d^-1 at high water level stage, respectively. Cyclotella hubeiana, Eudorina sp. and Cryptomonas ovata still kept larger growth rates at reservoir discharging stage. Their in situ growth rates were 0.231 ±0.012, 0.281 ±0.014 and 0.406 ±0.020 d^-1, respectively. Microcystis aeruginosa (with S growth strategy) turned out to be the dominant algae during this period for its increasing in situ growth rate during incubation. The main factors of in situ growth rate of algae were soluble reactive phosphorus(SRP) and water temperature in low water level stage. In high water level stage, particulate phosphorus and maximum wind speed were the main environmental factors. SRP, dissolved inorganic nitrogen and total nitrogen were the main environmental factors that impacted in situ growth rates of algae species in reservoir discharging stage. Regardless of the transport of algae with flow in and out of the research area, in situ growth rate of algae with different growth strategies has potential relationships with species succession pattern in the research area.