Autologous EpCAM-targeted CAR-T cell therapy (IMC001) was developed for advanced gastric cancer (GC). This study evaluated the specificity, efficacy, and safety of IMC001 in preclinical models and a phase 1 dose-escalation/expansion trial in patients who had failed at least two lines of therapy. IMC001 specifically recognized EpCAM and exhibited potent anti-tumor activity in EpCAM+ tumor cells, xenograft models, and patient-derived organoids. From August 2021 to May 2023, 12 advanced GC patients received IMC001. All patients experienced grade 3 or 4 treatment-related adverse events, mainly lymphopenia related to lymphodepletion, with no treatment-related deaths. Five patients experienced cytokine release syndrome (n = 3, grade 3-4) and two patients experienced immune-related hepatitis (n = 1, grade 3 in middle-dose group; n = 1, grade 4 in high-dose group). Partial responses were observed in 33.3% (1/3) of low-dose patients and 40% (2/5) of middle-dose patients, achieving an objective response rate of 30% and a disease control rate of 70%. Median progression-free survival and overall survival were 4.5 and 8.4 months, respectively. One patient underwent conversion surgery at week 27 and remains alive 31.5 months post-infusion. These findings demonstrate an acceptable safety profile and promising efficacy of IMC001 in advanced GC, supporting further clinical development for refractory GC patients.