The regional origin of Chinese wines was investigated using two important complementary techniques, site‐specific natural isotopic fractionation nuclear magnetic resonance (SNIF‐NMR) and isotope ratio mass spectrometry (IRMS). Twenty samples from five different grape varieties were collected from north Xinjiang in 2009, along with 100 wine samples from five different regions during 2010–2013. The (D/H)_I and (D/H)_II in wine ethanol ranged from 95.10 to 102.86 ppm and from 115.99 to 126.39 ppm using SNIF‐NMR, respectively. The ¹³C/¹²C of wine ethanol and ¹⁸O/¹⁶O of wine water were detected using IRMS. The δ¹³C value (−23.36‰) in coastal regions was higher than that in continental regions (−27.75‰). The temperature is the key for δ¹³C value. The δ¹⁸O ranged from −1.94 to 4.57‰. The δ¹⁸O values were only positive in north Xinjiang which had the arid climate and strong sunshine. No difference was found for isotope ratios for wines made from five different grape varieties in north Xinjiang. All data evaluated by principal component analysis and linear discriminant analysis showed that the best method to distinguish the regional wine origin correctly is a combination of (D/H)_I, (D/H)_II, R, δ¹³C and δ¹⁸O. Therefore, natural multi‐elemental isotope ratios are effective in contributing to wine quality control in the Chinese market.