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Unruptured intracranial aneurysms are common neurovascular diseases, and flow diverters (FDs) have emerged as a key treatment modality. However, in-stent stenosis (ISS) remains a frequent complication after FD treatment, increasing the risk of thromboembolic events. Thrombin time (TT), a critical coagulation indicator, has potential associations with ISS risk. The objective of this study was to investigate the relationship between TT and ISS risk, with a focus on potential threshold effects. This multicenter retrospective cohort study included 389 patients with unruptured intracranial aneurysms treated with FD between March 2016 and October 2024. The primary exposure was preoperative TT, and the primary outcome was ISS occurrence during follow-up. Generalized additive models were used to explore non-linear relationships, while segmented linear regression identified threshold points. ISS occurred in 22.62% (88/389) of patients. TT exhibited a non-linear relationship with ISS risk, with a threshold of 19.2 s. For TT values below this threshold, each unit increase was associated with a 59% higher likelihood of developing ISS (OR = 1.59, 95% CI: 1.19-2.13, p = 0.002). These findings may help identify patients at higher risk for ISS who could benefit from more intensive angiographic follow-up with shortened intervals, enabling earlier detection and timely intervention.