We investigated the association among metabolically healthy obesity (MHO), cardiovascular disease (CVD)risk, and all-cause mortality in the Asian population. We searched databases from inception to 16 November, 2019 and pooled data using a random-effects model. Subgroup analysis was conducted according to the following comparison groups: MHNW (without overweight or underweight participants) and MHNO (non-obese, including overweight and underweight participants). Nineteen studies were included. The mean Newcastle–Ottawa Scale score was 7.8. Participants with MHO had a significantly higher CVD risk (odds ratio (OR) = 1.36, 95% confidence interval (CI) = 1.13–1.63) and significantly lower risk of all-cause mortality (OR = 0.88, 95% CI = 0.78–1.00) than the comparison group. Subgroup analyses revealed participants with MHO had a significantly higher CVD risk than MHNW participants (OR = 1.61; 95% CI = 1.24–2.08; I2 = 73%), but there was no significant difference compared with MHNO participants (OR, 1.04; 95% CI, 0.80–1.36; I2 = 68%). Participants with MHO had a significantly lower risk of all-cause mortality (OR = 0.83; 95% CI = 0.78–0.88; I2 = 9%) than MHNO participants, but a borderline significantly higher risk of all-cause mortality than MHNW participants (OR = 1.30; 95% CI = 0.99–1.72; I2 = 0%). The CVD risk and all-cause mortality of the MHO group changed depending on the control group. Thus, future studies should select control groups carefully.