Objective To investigate the incidence of suicidal ideation and its influencing factors among freshmen of the three public comprehensive university in Nanjing. Methods Questionnaires were given to 8 811 freshmen of the three public comprehensive university in Nanjing， including general information （age， gender， parental divorce， previous history of psychosis， suicide history， etc.）， Neuroticism component of Eysenck Personality Questionnaire（ EPQ-N）， Adolescent Self-rating Life Events Checklis（t ASLEC）， subjective support and social support availability component of Social Support Rating Scale（ SSRS） and Beck Depression Inventory（BDI）. Logistic regression model was used to analyze the influencing factors of suicidal ideation. Results Among the 8 811 freshmen， 8 770 valid questionnaires were collected， among which 7 754（ 88.4%） had no suicidal thoughts and 1 016（ 11.6%） had suicidal thoughts. Multivariate logistic regression results showed that young age（ OR=0.913， 95%CI： 0.876-0.952）， female（ OR=1.296， 95%CI： 1.093-1.535）， parental divorce （OR=1.366， 95%CI： 1.034-1.804）， previous history of mental illness（ OR=1.957， 95%CI： 1.445-2.652）， previous suicide history（ OR=4.827， 95%CI： 3.195-7.293）， depression（ OR=3.982， 95%CI： 3.384-4.685）， high neuroticism score（ OR=1.172， 95%CI： 1.142-1.202）， low levels of SSRS subjective social support and the utilization of social support（ OR=0.936， 95%CI： 0.916-0.955）， more negative life events（ high ASLEC score， OR=1.020， 95%CI： 1.013-1.027） were independent risk factors of suicidal ideation（ all P ＜ 0.05）. Conclusions The incidence of suicidal ideation among freshmen is high， and the influencing factors are diverse and complex. Therefore， it is necessary to prevent and intervene the suicidal ideation of freshmen from multiple perspectives， such as individual demographic characteristics， family， psychological characteristics and society.