Shares in the company fell by over 3% in early trade.
TotalEnergies' European Refining Margin Marker stood at $15.4/t in the third quarter of the year, down from $44.9/t the previous quarter.
A drop in refining margins in recent months, a result of slowing global economic activity and new refineries coming online, is set to weigh on third-quarter earnings of the world's top energy companies.
BP, Shell and Exxon Mobil this month issued similar warnings, as oil prices fell 17% in the third quarter — the largest quarterly decline in a year — on worries about the global oil demand outlook.
Total's overall quarterly hydrocarbon production is expected to be at 2.4 million barrels of oil-equivalent per day (Mboe/d), at the lower end of guidance given in second-quarter results.
The company cited security-related disruptions in Libya, where a dispute between rival governments caused oilfield shutdowns, and an August outage at the Australian Ichthys LNG plant, in which Total holds a 30% stake, which left the site running at half-capacity into October.
That loss of production was partly offset by ramping up the 180kb/d Mero 2 oil development in Brazil, where Total holds a 19.3% stake.