Only 40 percent of high-speed TGV services will be running, and just one in four regular trains across the country, SNCF chief Guillaume Pepy told RTL radio.
Outside Paris, just one in three SNCF trains serving the outlying suburbs is expected as unions protest an overhaul that would strip new hires of a special status that guarantees early retirement and other benefits.
Four Eurostar trains between London and Paris have already been cancelled.
"We're going to do everything possible to help passengers," Pepy said, adding that the SNCF's national headquarters and regional offices would be closed in order to free up personnel.
In Paris itself, metro and bus services are set to run normally, but some suburban commuter lines will be affected, with just two out of three trains scheduled during rush hours on the heavily used RER A and B lines.
France's civil aviation authority said a third of flights into and out of the main Paris airports of Charles de Gaulle, Orly and Beauvais would be cancelled Thursday because of a strike by air traffic controllers.
Air France said shorter flights would be the most affected, while all long-haul flights were currently expected to operate.
Those cancellations come ahead of a separate strike by Air France pilots and cabin crew Friday seeking a six-percent raise.
Teachers are also striking on Thursday, mainly at primary schools, as are hospital workers and some civil servants in the biggest test for Macron since a wave of demonstrations last September and October.
Warning by rail workers
More than 140 protests are planned across France, the biggest at the Bastille monument in central Paris where unions expect 25,000 demonstrators.
Public servants are angry over pay that has not kept up with inflation, while unions accuse Macron of wanting to take a sledgehammer to the public sector.
Macron has pledged to cut 120,000 public jobs during his five-year term and his government has raised the prospect of voluntary redundancies, prompting fears that the quality of services will take a hit.
Plans to use more contractors and increasingly offer pay based on merit, rather than on experience, are seen by unions as attacks on traditional job security.
On the railways, plans to strip new recruits of a guaranteed job for life and other benefits have riled unionists who also fear that a restructuring of the SNCF could eventually see it privatised.
They have announced a three-month wave of intermittent strikes to try to force the government to back down, vowing two days of strikes every five days.
But a leaked letter from an official at the hardline CGT union, the biggest at the SNCF, suggested that workers were preparing more severe disruptions.
"The disarray to operations will also affect the days when we're working," since trains and agents often won't be where they are supposed to be, according to the letter.
"Management will be totally lost and unable to anticipate anything," making it impossible to accurately warn users of disruptions for the next day, as the SNCF has promised.
Transport Minister Elisabeth Borne responded on RMC radio: "I cannot believe rail workers would support such methods."