The invention discloses a detection system for an obstructive sleep apnea syndrome based on an HRV frequency domain analysis. The detection system is formed by an electrocardiosignal collection module, an electrocardiosignal pre-processing module, a heartbeat interval extraction module, a heartbeat interval pre-processing module, a network switching module and a topology feature calculating module, wherein the electrocardiosignal collection module acquires an ECG signal during the sleep of a patient; the electrocardiosignal pre-processing module can filter noise and baseline drift via a band-pass filter; the heartbeat interval extraction module detects a R wave to acquire an HRV signal; the heartbeat interval pre-processing module filters the HRV signal and leach abnormal values; a network generation module switches the HRV signal into N segments to build an un-weighted and undirected network; and the topology feature calculating module calculates a topology feature value of the un-weighted and undirected network, and determines an optimal threshold value for topology feature value work. The operation method of the detection system is simple and high detection accuracy can be achieved.