Elevated resting heart rate (RHR) predicts all-cause death. However, the relationship between RHR variation over years and mortality are still unknown. We aimed to analyze the association between RHR variation and all-cause mortality in the general population without cardiovascular diseases. A total of 46,873 subjects were included from the Kailuan Study (2006-2011). RHR readings were taken during three separate examinations and the RHR variation was defined using the standard deviation (RHR-SD) and the coefficient of variation. Participants were divided into four groups according to the quartiles of RHR-SD. All subjects were followed for a median of 49.4 months from the date of the 3rd examination to December 31, 2014. Up until the follow-up examinations, 973 (2.08%) participants had died. In a multivariate analysis, adjusting for variables potentially associated with death, the highest quartile of RHR-SD remained an independent predictor of all-cause mortality (Hazards ratio = 1.43, 95% confidence interval 1.18-1.74, P < 0.001). These findings suggest that an elevated long-term RHR variation is an independent risk marker for all-cause mortality in the general population without known cardiovascular diseases.