This study found Cystatin SN (CST1), a type 2 cystatin subfamily member, to be highly expressed in nasal polyps from patients with intractable chronic rhinosinusitis with nasal polyps (CRSwNP), using a whole transcript analysis with next-generation sequencing. Eosinophilic chronic rhinosinusitis (ECRS) involves nasal polyps that are refractory and recurrent immediately after endoscopic sinus surgery (ESS). We hypothesized that CST1 may contribute to the pathogenesis of ECRS. The expression of CST1 in nasal polyps from patients with ECRS was examined by mRNA expression levels, using real-time PCR and immunohistochemistry. CST1 was significantly expressed in the epithelial cells of the nasal polyps from patients with ECRS, compared with patients who did not have ECRS (non-ECRS). Particularly, CST1 showed very strong expression in patients with severe ECRS. The expression of CST1 may be correlated with the recurring and refractory nature of ECRS. We examined the function of CST1 using nasal epithelial cells and nasal fibroblasts. Stimulation by a combination of IL-4 plus dsRNA plus CST1 significantly elevated mRNA expression levels and protein levels of TSLP in nasal epithelial cells. Stimulation by TSLP or IL-33 significantly elevated mRNA expression levels of CST1 in nasal epithelial cells. Stimulation of CST1 significantly elevated mRNA expression levels of CCL11 and periostin in nasal fibroblasts. CST1 could amplify eosinophilic infiltration and Th2 inflammation by interacting with epithelial-derived cytokines and fibroblasts on nasal polyps. CST1 may be involved in the pathogenesis of ECRS, and may contribute to the severity and recurrence of CRSwNP after ESS.