Aerial photography is widely accepted as a useful method for monitoring penguins in Antarctica, but there are concerns about the disturbance it causes to penguins in the process. Since 2016, aerial photography using unmanned aerial vehicles (UAVs) has been carried out by Korean scientists to count Adélie penguins’ nests at Cape Hallett, but the impact of using this method on breeding penguins has not been investigated. An annual survey should be conducted to determine the population size of Adélie penguins in this area, because Cape Hallett was designated as a new site for the Ecosystem Monitoring Program (CEMP) of the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) in 2018. In order to obtain suitable images for counting the number of nests and mitigate disturbances derived from UAV operation, we compared the difference of the penguins’ behavioral responses to UAVs’ approaches by flight altitude and type (hexacopter and quadcopter). Based on penguins’ responses to visual approaches and noises of UAVs, we hereby suggest 50 m and 100 m as minimum flight altitudes for quadcopters and hexacopters, respectively, when monitoring penguins.