Highly sensitive protein biomarker detection is critical for the diagnosis of gastric cancer (GC), however the accurate and sensitive detection of low-abundance proteins in early-stage GC is still a challenge. Herein, a surface-enhanced Raman scattering frequency shift assay was performed on a developed microfluidic chip for the detection of GC protein biomarkers carcinoembryonic antigen (CEA) and vascular endothelial growth factor (VEGF). The chip is made up of three groups of parallel channels and each parallel channel consists of two reaction regions, enabling the simultaneous analysis of multiple biomarkers in multiple samples. The presence of CEA and VEGF in the sample can be captured by the 4-mercaptobenzoic acid (4-MBA)-conjugated antibody functionalized gold nano-sheet (GNS-) substrate, resulting in the Raman frequency shift. As a result, a typical Raman frequency shift of 4-MBA presented a linear relationship with the concentration of CEA and VEGF. The limit of detection (LOD) of the proposed SERS microfluidic chip reaches as low as 0.38 pg mL-1 for CEA and 0.82 pg mL-1 for VEGF. During the detection process, only one step of sample addition is involved, which eliminates the multiple reaction step-induced nonspecific adsorption and significantly increases the convenience and specificity. In addition, serum samples from GC patients and healthy subjects were tested and the results were in good agreement with the current gold-standard method ELISA, suggesting the potential application of the SERS microfluidic chip in clinical settings for early diagnosis and prognosis of GC.