Background: Upadacitinib (UPA) is a new small-molecule drug for treating inflammatory bowel disease (IBD); however, its therapeutic use in China remains limited. Objectives: This study aimed to explore Chinese physicians’ treatment preferences for UPA in IBD and analyze experience-related decision-making differences. Design: A nationwide cross-sectional study conducted among Chinese physicians. Methods: The study was conducted among Chinese physicians using a 69-item questionnaire on physicians’ backgrounds and UPA preferences, covering (1) Physician backgrounds (12 items), (2) Therapeutic preferences regarding physicians’ attention to different characteristics of UPA and physicians (24 items), and (3) clinical application practices (33 items). Physicians were categorized into experienced and inexperienced groups, and preference differences were compared and analyzed using chi-square or Fisher’s exact tests. Results: Of 583 participating physicians, 182 were classified as experienced and 401 as inexperienced. Safety and efficacy were prioritized by 63.8% and 61.6% of physicians, respectively. UPA was preferred for patients with IBD aged 18–60 years (452/583, 77.5%) and with moderate-to-severe disease activity (486/583, 83.4%). For clinical application, experienced physicians preferred efficacy assessments at week 8 (63/182, 34.6%), while inexperienced physicians preferred week 12 (133/401, 33.2%) for patients with ulcerative colitis. Both groups preferred week 12 for efficacy assessments (251/583, 43.0%) and evaluation of perianal involvement (269/583, 46.1%) and extraintestinal manifestations (271/583, 46.5%) in Crohn’s disease. Safety concerns included thrombosis, opportunistic infections, and severe infections, with discontinuation recommended for severe infections, cardiovascular events, or thrombosis. Conclusion: This was the first nationwide cross-sectional study to investigate the therapeutic preferences of Chinese physicians for UPA in patients with IBD. These findings provide evidence-based support for UPA applications in China but require further real-world validation.