The UN human rights agency says it has documented arbitrary arrests, torture and at least one extra-judicial execution in the region.
"There is an urgent need for accountability," UN human rights chief Zeid Ra'ad Al Hussein said.
Russia annexed the peninsula from Ukraine after the country's pro-Russian leader was overthrown in 2014.
There was no immediate response from Russia to the report's accusations.
"Grave human rights violations, such as arbitrary arrests and detentions, enforced disappearances, ill-treatment and torture, and at least one extra-judicial execution were documented," the report says.
It adds that there have been "intrusive law enforcement raids of private properties" which "interfered with [the] right to privacy".
The report, which says the human rights situation has "significantly deteriorated" in the region, notes that hundreds of prisoners were illegally transferred from Crimea to Russian jails.
It says civil servants were forced to renounce their Ukrainian citizenship or face losing their jobs, and condemned Moscow's decision to replace Ukrainian laws with Russian ones.
"Education in Ukrainian has all but disappeared from Crimean schools," the report adds.
It is based on interviews conducted from mainland Ukraine, as human rights investigators were not permitted entry into the region.
Crimea, which has a Russian-speaking majority, voted to join Russia in a referendum that Ukraine and the West deem illegal.
The UN says Crimea's Turkic-speaking minority, the Tatars, who make up 12% of its population, have been targeted.
The Tatar parliament, the Mejlis, boycotted the referendum on joining Russia. Moscow said it was an extremist organisation and banned it last year.
"While those human rights violations and abuses have affected Crimean residents of diverse ethnic backgrounds, Crimean Tatars were particularly targeted especially those with links to the Mejlis", the UN report says.
It adds that the ban on the Mejlis "has infringed on the civil, political and cultural rights of Crimean Tatars".
Hussein accused Russia of failing to investigate alleged human rights violations.
He said: "Failure to prosecute these acts and ensure accountability has denied victims of proper remedy and strengthened impunity, potentially encouraging the continued perpetration of human rights violations.".