"It was an intentional attack on LGBT people," he said.
Longhurst said it was more of an attack on all humans, like what happened at the Bataclan during the Paris attacks, and Jones hit back and said the host didn't understand because he wasn't gay.
Longhurst said "whether I'm gay or not has no reflection on the fact this person killed 50 people".
Co-panellist discussing the Orlando massacre, Julia Hartley-Brewer, also debated with Jones about whether it was an intentional attack on the LGBTI community.
She told him he didn't have ownership of the horror of the crime just because he was gay.
She also said we did not know how much of the attack was motivated by homophobia, and it was all speculation.
Clearly frustrated by the conversation as Longhurst and his co-panellist talk over the top of him, Jones gets out of his chair and says "I've had enough of this" and removes his microphone.
Hartley-Brewer tried to calm him down by saying they were just trying to have a civilised conversation and acknowledged he was upset.
"Everyone is upset and angry about this, but storming off a TV set ... " she said.
Viewers commended Jones on Twitter for walking off.
"It was actually vile, I've never seen such dismissive, heartless interviewing," one commented.
The attack on the Orlando nightclub was the worst shooting in US history and said to be the worst attack since 9/11.
Mateen called 911 and pledged his allegiance to Islamic State before gunning down people in the club.
Longhurst questioned whether the shooting was a hate crime or something done in the name of religion.
"It's both," Jones said.
"People rationalise their hatred, this guy [the gunman] apparently according to his dad saw two men kissing and he was repulsed by it, people know this who are gay, but there are people like that who are sickened and repulsed by our very existence and this guy, however he dresses up his bigotry and hatred, he's somebody who hates gays, he hates LGBT people."
Jones said Mateen used the gun to murder LGBT people.
"At the end of the day this was a homophobic hate crime as well as terrorism," he said.