A meta-analysis of prospective studies was conducted to examine the association of total, supplemental, and dietary magnesium intakes with risk of all-cause, cancer, and cardiovascular disease (CVD) mortality and identify the dose-response relations involved in these association. We performed a systematic search of PubMed, Scopus, Google Scholar, and ISI Web of Knowledge up to April 2020. Prospective cohort studies that reported risk estimates for the association between total, supplemental, and dietary magnesium intakes and risk of mortality were included. Random effects models were used. Nineteen publication with a total of 1,168,756 participants were included in the current meta-analysis. In total, 52,378 deaths from all causes, 23,478 from CVD, and 11,408 from cancer were identified during the follow-up period of 3.5 to 32 years. Dietary magnesium intake was associated with a lower risk of all-cause [pooled effect size (ES): 0.87; 95% CI: 0.79, 0.97; P = 0.009; I2 = 70.7%; P < 0.001] and cancer mortality (pooled ES: 0.80; 95% CI: 0.67, 0.97; P = 0.023; I2 = 55.7%; P = 0.027), but not with CVD mortality (pooled ES: 0.93; 95% CI: 0.82, 1.07; P = 0.313; I2 = 72.3%; P < 0.001). For supplemental and total magnesium intakes, we did not find any significant associations with risks of all-cause, CVD, and cancer mortality. However, linear dose-response meta-analysis indicated that each additional intake of 100 mg/d of dietary magnesium was associated with a 6% and 5% reduced risk of all-cause and cancer mortality, respectively. In conclusion, higher intake of dietary magnesium was associated with a reduced risk of all-cause and cancer mortality, but not CVD mortality. Supplemental and total magnesium intakes were not associated with the risk of all-cause, CVD, and cancer mortality. These findings indicate that consumption of magnesium from dietary sources may be beneficial in reducing all-cause and cancer mortality and thus have practical importance for public health.