Lymph node metastasis is the major concern that causes death in colorectal cancers. However, biomarkers for cancer metastasis are still lacking. In this study, we applied an LC-MS/MS-based label-free quantitative proteomics approach to compare the differential secretome of a primary cell line SW480 and its lymph node metastatic cell line SW620 from the same colorectal cancer patient. We identified a total of 910 proteins from the conditioned media and 145 differential proteins between SW480 and SW620 (>1.5-fold change). The differential expression pattern of 6 candidate proteins was validated by Western blot analysis. Among them, trefoil factor 3 and growth/differentiation factor 15, two up-regulated proteins in SW620, were further analyzed in a large cohort of clinical tissue and serum samples. Sandwich ELISA assay showed that the serum levels of both proteins were significantly higher in lymph node metastatic colorectal cancers. Receiver operating characteristic curve analysis confirmed that serum trefoil factor 3 and growth/differentiation factor 15 could provide a discriminatory diagnostic test for predicting colorectal cancer metastasis. Immunohistochemical analysis also showed that the overexpression of trefoil factor 3 or growth/differentiation factor 15 in colorectal cancer was associated with lymph node metastatic behavior. This study showed an accurate, sensitive, and robust label-free quantitation approach for differential analysis of cancer secretome. The comparison of the cancer secretome in vitro is a feasible strategy to obtain valuable biomarkers for potential clinical application. Both trefoil factor 3 and growth/differentiation factor 15 could serve as potential biomarkers for the prediction of colorectal cancer metastasis.