Nova SMC 2016 has been the most luminous nova known in the direction of the Magellanic Clouds. It turned into a very luminous supersoft X-ray source between day 16 and 28 after the optical maximum. We observed it with Chandra, the HRC-S camera and the Low Energy Transmission Grating (LETG) on 2016 November and 2017 January (days 39 and 88 after optical maximum), and with XMM-Newton on 2016 December (day 75). We detected the compact white dwarf (WD) spectrum as a luminous supersoft X-ray continuum with deep absorption features of carbon, nitrogen, magnesium, calcium, probably argon and sulfur on day 39, and oxygen, nitrogen and carbon on days 75 and 88. The spectral features attributed to the WD atmosphere are all blue-shifted, by about 1800 km s −1 on day 39 and up to 2100 km s −1 in the following observations. Spectral lines attributed to low ionization potential transitions in the Corresponding author: Marina Orio