The invention discloses a container data center cooling system and an operation strategy thereof, and belongs to the technical field of energy conservation. The system comprises a box body inner water cooling circulation module, a fresh air natural cooling module, a hot water tank, a sky radiation refrigeration module, a water side natural cooling module, a cold water tank, a steam compression refrigeration module, a water storage tank, a first electromagnetic three-way valve, a second electromagnetic three-way valve, a first three-way connector and a second three-way connector. According to the container data center cooling system, the sky radiation refrigeration technology is combined into the container data center cooling system, the coupling condition of multiple cold sources is considered, scientific integrated optimization design is conducted on wide-area all-weather application of the container data center cooling system, and the temperature sensors, the flow meters, the valves and the bypass pipelines are additionally arranged, so the operation conditions are monitored in real time, cooling modes are flexibly switched according to internal and external parameters of the system, natural cold sources are fully utilized, refrigeration energy consumption is reduced, and energy and economic benefits are improved. Meanwhile, flexible movement and rapid construction and installation capability of the container data center are ensured.