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The impact sparked panic, as some passengers feared a jihadist attack was underway, according to one witness.
The regional express was carrying 219 passengers on a service between Nimes and Montpellier when it hit the tree at 140 kilometres (87 miles) per hour, the state rail operator SNCF said.
The accident occurred near the town of Lunel, about 28 km southwest of Nimes.
A critically-injured individual was airlifted to hospital, according to the head of local rescue services, Christophe Risdorfer. Fifty other passengers suffered minor injuries or shock.
“We were on the train when hailstones the size of ping-pong balls started falling, then we heard what sounded like an explosion,” said a 24-year-old passenger from Luxembourg who gave her name as Justine.
“The train shook for a few seconds and then I saw some people whose heads were covered in blood.”
Another passenger said some people on the train feared a jihadist attack was unfolding.
A string of terror assaults in Europe in recent months has left the continent on edge.
“There was panic, some at first thought it was an attack on the train,” said the 35-year-old woman named Virginie.
SNCF said around 80 rescue workers, backed by helicopters, were deployed to the scene, where “access is very difficult.”
The tree was a “very tall pine” located on private property next to the railway line, the company said.
Despite the impact, the train did not derail and traffic was expected to resume later Wednesday on one of the tracks of the line.