This large-scale survey aimed to evaluate frequencies and patterns of Chinese herbal medicine (CHM) used for Sjögren's syndrome (SS) in Taiwan by analyzing the National Health Insurance Research Database (NHIRD) for cases in which CHM was used as an alternative therapy to Western medicine for improving patients' discomforts. We analyzed cases of SS principal diagnosis (ICD-9:710.2) with a catastrophic illness certificate (CIC) in traditional Chinese medicine (TCM) outpatient clinics from three cohorts of the Longitudinal Health Insurance Database (LHID) in the NHIRD between 2002 and 2011. CHM prescription patterns for SS were evaluated from claimed visitation files and corresponding prescription files. There were 15,914 SS patients with CIC (SS/CIC), and we found only 130 SS/CIC cases visiting TCM clinics in LHID2000, 133 in LHID2005, and 126 in LHID2010. After removing duplicate data, 366 SS/CIC and 4,867 visits were analyzed. The 50–59 year age group showed the highest ratio (29.51%) in both women and men. “Qi-Ju-Di-Huang-Wan” and “Xuan-Shen” (Scrophularia ningpoensis Hemsl.) was the most commonly used formula and single herb, respectively. “Qi-Ju-Di-Huang-Wan, Gan-Lu-Yin, Xuan-Shen, Mai-Men-Dong (Ophiopogon japonicus (L. f.) Ker-Gawl.), and Sheng-Di-Huang (raw Rehmannia glutinosa Libosch)” were the core pattern prescriptions in treating SS/CIC.