Beijing ranked last in the poll, with Shanghai taking 89th place and Hong Kong 83rd.
The survey was conducted by the Germany-based rented housing website Nestpick in 80 countries around the world.
About 2,500 people in the LGBT community were surveyed in each city before the final 100 shortlist was compiled.
People polled were asked about several criteria, including the strength of a city’s dating scene, nightlife, the openness of fellow citizens towards their sexual orientation, safety and the rights granted to the lesbian, gay, bisexual and transgender community.
The top three cities in the poll were Madrid, Amsterdam and Toronto.
The survey was published on Wednesday to mark the 48th anniversary of the Stonewall Riots in New York that were sparked by a police raid on a gay bar. The riots are now viewed as a key event in the campaign for gay rights.
A Gay Pride parade will be held in many cities around the world this month, but none in mainland China.
Hong Kong, Shanghai and Beijing all received the lowest polling for LGBT rights. Gay people do not have the legal right to marry in Hong Kong and mainland China.
Beijing also performed poorly on safety for the LGBT community. It scored only 1.84 out of five.
The capital was rated 2.15 for its gay dating scene, 2.12 for nightlife and 2.03 on fellow citizens’ openness. Shanghai was rated 2.51 for its openness towards the LGBT community.
Carol Ding, a Guangzhou-based lawyer who belongs to Rainbow Lawyers Group, an organisation that supports LGBT rights, said she was surprised Chinese cities were included in the world’s 100 best cities for LGBT people.
“I think it’s a far cry for these cities to be regarded as friendly towards the LGBT community,” said Ding. “The personal safety of gay people is even not guaranteed.”
She said many people in mainland China still think that LGBT people were mentally ill. Some hospitals in big cities offer “corrective” treatment for people who are open about their sexual orientation and are sent by force to these institutions.
Jean Ouyang, a 24-year-old lesbian living in Beijing, said there were few lesbian bars in the capital compared with gay bars.
She added that very few events were held to mark Gay Pride this month, with some only held at foreign embassies in Beijing.
“For most of the public, they don’t know of the existence of the LGBT community,” she said.
Male transvestites wearing women’s clothing were often attacked on the street in Beijing as their appearance was deemed to contravene mainstream values, she added.
Adam Tang, a manager at a financial firm in Shanghai, said he was unaware if any of his friends or colleagues were gay.
“If he or she opens their identity, I won’t change my attitude towards them because I judge a person based on their personality, not on their sexual orientation,” he said.
He added that he holds a neutral position on whether gay marriage should be legalised in mainland China.
However, he said a trip to London showed him how conservative values were in China.
“There was a male couple walking hand in hand in front of us. I really felt embarrassed at that moment,” he said.
London was ranked fifth in the 100 best LGBT cities ranking.