Epidermal growth factor receptor (EGFR)-targeted therapy represents an important approach in metastatic colorectal cancer (CRC) therapy. However, a number of CRC patients show intrinsic or acquired resistance to EGFR-targeted therapy. EGFR antibody therapy is established in CRC patients with wild-type KRAS. However, up to half of these patients do not respond to this therapy. This phenomenon implied some potential mechanisms of resistance to EGFR inhibitors might exist. One of the potential reasons to explain this phenomenon is heterogeneity of CRC. The heterogeneity of CRC has been well described at the morphological, molecular and genomic levels. This review discussed the potential relationship of heterogeneity, including intratumor heterogeneity of CRC and heterogeneity in primary CRC and its corresponding metastases, to EGFR-targeted therapy failure.