Little is known about stroke with different obesity phenotype as determined using the Adult Treatment Panel-III criteria with metabolic health or not. This study aimed to investigate the effects of metabolically healthy and unhealthy obesity on ischemic stroke in a general population. A total of 11,150 adults were examined using a multi-stage cluster sampling method to select a representative sample of individuals 35 years or older. Ischemic stroke was defined as history of a cerebrovascular event, as documented by doctors via either cranial CT or MR scan within the past 2 years. All subjects were categorized as having metabolically healthy non-obesity (MHNO), metabolically unhealthy non-obesity (MUNO), metabolically healthy obesity (MHO) or metabolically unhealthy obesity (MUO) using the Adult Treatment Panel-III criteria. Stratified analysis were done based on different body mass index group. For the total population, multiple regression analyses revealed that individuals with MUNO and MUO were more likely to experience ischemic stroke compared with those with MHNO (OR 2.136, 95 % CI 1.677–2.720; OR 2.712, 95 % CI 1.798–4.092; all p < 0.001). The OR for ischemic stroke did not significantly differ between MHO and MHNO. Stratification based on different BMI group showed that, compared with people who were normal weight without Mes, participants who were in Mes with overweight or obesity had significantly higher OR for ischemic stroke(both p < 0.05); participants who were not in Mes with overweight or obesity did not showed OR significantly higher. Ischemic stroke is likely associated with poor metabolic health rather than with obesity itself.