Objective: To compare the differences in heart rate variability (HRV) indicators between depressive college students with and without suicidal ideation, so as to provide a reliable objective physiological basis for suicide screening and prevention among college students. Methods: From March to April 2023, a total of 60 college students with depression aged 17-25 years old were recruited from three universities in Daqing City, Heilongjiang Province through online and campus recruitment. They were divided into the depression with suicidal ideation group (30 cases) and the depression without suicidal ideation group (30 cases) based on the presence of suicidal ideation. A screening survey was conducted on college students using a self designed general information questionnaire, Hamilton Depression Scale (HAMD), and Scale for Suicide Ideation (SSI). In May 2023, 5 minute resting HRV data was collected from the two groups of participants, and statistical analysis was conducted using t-tests or MannWhitney U tests. Results: The SSI and HAMD scores of college students in the depression group with suicidal ideation [7.00(4.25, 16.00), 40.73±12.88] were higher than those in the depression group without suicidal ideation [4.50(1.75, 6.00), 29.17±8.15 ] ( Z/t= -6.64 , 4.16, P <0.01). The standard deviation of the NN (SDNN), standard deviation of the average NN intervals (SDANN) and standard deviation of the NN interval every 5 minutes (SDNN Index) in the HRV time domain indicators of college students with depression and suicidal ideation [42.75(35.03, 60.75)ms, 32.75(26.65, 46.88)ms, (298.82±61.61)ms] were lower than those in the depression without suicidal ideation group [50.80(46.15, 59.68)ms, 38.80(34.50, 45.80)ms, (329.20±50.80)ms] ( Z/t= -2.43 , -2.20, -2.08, P <0.05). The very low frequency (VLF) in frequency domain indicators of college students with depression and suicidal ideation [0.02(0.02,0.02)Hz] was higher than that in the depression group without suicidal ideation [0.02(0.01, 0.02 )Hz] ( Z=-2.19, P <0.05). Conclusions College students with suicidal ideation have higher levels of depression and imbalanced autonomic nervous system function, and HRV may become an objective physiological indicator for identifying suicidal ideation.