The present invention discloses a skylight operating system of a modular data center, so as to timely respond to a firefighting requirement of the modular data center to reduce occurrence of firefighting-related accidents. The skylight operating system comprises: an electric skylight; a firefighting environment index monitoring device arranged inside the modular data center; a monitoring and interacting device arranged in a monitoring room outside the modular data center, and connected with the electric skylight and the firefighting environment index monitoring device, the monitoring and interacting device adapted for receiving monitoring information of the firefighting environment index monitoring device, and opening the electric skylight upon determination that a firefighting-related issue occurs inside the modular data center.