The invention discloses combined application of cystatin S and carcinoembryonic antigen (CEA), and specifically discloses application of cystatin S and CEA to prepare a marker for diagnosing and indicating stomach cancer or gastrointestinal stromal tumor. The invention also discloses a trapping agent of the marker of stomach cancer or gastrointestinal stromal tumor and a kit containing the trapping agent. The kit has the advantages of being good in specificity, high in sensitivity and the like, is applicable to early diagnosis on stomach cancer or gastrointestinal stromal tumor, assessment on treatment effect during treatment and monitoring on metastasis and recurrence after treatment is finished, and the diagnosis result is earlier than clinic symptoms.