Incomplete fatty acid oxidation leads to accumulation of intermediates such as acylcarnitines. The aim of this study was to investigate associations of carnitine and acylcarnitines with development of metabolic syndrome (MetS) in a middle‐aged and older Chinese population. In 2005, 3289 participants, aged 50‐70 years, were recruited from Beijing and Shanghai, China, and were resurveyed in 2011. Concentrations of baseline plasma free carnitine and acylcarnitines were quantified using liquid chromatography‐tandem mass spectrometry. After 6‐year follow up, 421 out of 1208 participants without MetS at baseline developed MetS. Free carnitine, propionylcarnitine, valerylcarnitine, octanenoylcarnitine, palmitoylcarnitine and 3‐Hydroxy‐octadecenoyl carnitine were each statistically significantly associated with incident MetS after correction for multiple testing. In a stepwise logistic regression including all of these (acyl)carnitines simultaneously, only free carnitine and octanenoylcarnitine remained significantly associated with incident MetS. Compared with those in the first quartile of free carnitine, those in the fourth quartile had 2 fold increased risk [odds ratio: 2.00, 95% confidence interval (CI): 1.40, 2.86] for incident MetS. Similar trend was observed for octanenoylcarnitine [OR, 95% CI: 2.21 (1.56, 3.14) comparing extreme quartiles]. In conclusion, accumulation of free carnitine and octanenoylcarnitine may increase the risk of MetS in middle‐aged and older Chinese adults.