Provided are a multi-channel fluorescence detecting module and a nucleic acid analysis system including the multi-channel fluorescence detecting module. The nucleic acid analysis system includes: a plurality of loaders configured to accommodate a plurality of cartridges respectively, the cartridges comprising microfluidic devices; a transfer module including a linear actuator, the linear actuator including a movable unit configured to move linearly; and a fluorescence detecting module fixed to the movable unit, the fluorescence detecting module being configured to emit excitation light to the cartridges and detect fluorescence emitted from samples on the cartridges. The loaders are arranged in a row in a linearly moving direction of the movable unit.