Proper medication management is crucial in metastatic colorectal cancer because of its substantially low survival rate. There has been advancing evidence on the efficacy of the two most prescribed targeted agents (bevacizumab and cetuximab); however, comprehensive analyses on their safety are limited. This study aims to comprehensively assess the clinical safety of first-line bevacizumab and cetuximab-based chemotherapy in unresectable RAS wild-type metastatic colorectal cancer patients and to provide guidance on the selection of appropriate targeted therapeutic agents. Keyword searches of MEDLINE, Cochrane Library, and ClinicalKey were conducted per PRISMA guidelines. We performed pooled analysis on safety outcomes from six studies which administered FOLFOX (5-fluorouracil, leucovorin, and oxaliplatin) or FOLFIRI (5-fluorouracil, leucovorin, irinotecan) as backbone chemotherapy. Thirty different adverse events from six categories were compared. First-line bevacizumab-based chemotherapy substantially lowered the risks of adverse events related to the dermatological (RR 0.24, 95% CI: 0.11–0.53, p < 0.00001) and renal systems (RR 0.57, 95% CI: 0.37–0.86, p = 0.007), while significantly increasing the incidence of cardiovascular adverse events (RR 4.65, 95% CI: 1.83–11.78, p = 0.001). Thus, first-line cetuximab-based chemotherapy increases patient susceptibility to dermatological and renal adverse events, especially with rash and electrolyte disorders, whereas bevacizumab-based chemotherapy increases cardiovascular risks such as hypertension and arrhythmia.