The court, which determines whether laws are constitutional, struck down 35 of the 80 measures contained in the bill.
Most of the scrapped clauses were introduced by opposition conservative lawmakers during a turbulent parliamentary process.
Measures, including making it harder for migrants to bring in relatives to live with them in France, for birth in France to lead to citizenship and to get access to state welfare, were scrapped for procedural reasons.
The ruling offers some relief to President Emmanuel Macron, who had made the bill a key plank of his second term.
Macron, who lacks a working majority in parliament, was embarrassed by the support it drew from Marine Le Pen's populist National Rally party as conservative MPs hardened its content.
Along with three other groups, Macron had referred the legislation to the Council.
Interior Minister Gerald Darmanin welcomed the ruling, saying it validated the government's initial proposals.
"Never has a bill included more measures to expel delinquents or introduced stricter requirements for the integration of foreigners," Darmanin added.
Gathered about a hundred metres away from the courthouse, a group of people opposed to the bill said they were still concerned despite the changes.
"We are a bit relieved but we remained worried - in the initial text there was lots of bad stuff," said Virgile Vaugelade, a school teacher in a Paris suburb, adding he expected the rejected measures would be added at another time.
Of the measures the court annulled, 32 were purely on procedural grounds.
The court did not not say whether the content of those clauses breached the constitution, meaning they could be introduced in a future bill.
Public law professor Serge Slama said that the ruling works in the government's favour while changing very little for migrant rights since the articles proposed by the conservative MPs were axed on procedural grounds, not on their content.
"They said as little as they could, while fulfilling their role to make sure procedure is respected," said Slama, professor at University Grenoble-Alpes, adding that this is commonplace in Constitutional Council decisions.
