The 39-year-old beat Merckx's mark, which had stood since 1975, on the fifth stage of this year's Tour near the Alps having equalled it in 2021.
"It's my 15th Tour de France and it takes a lot to get here, getting in shape every year," Cavendish said at the line.
"I'm surrounded by incredible people and I owe a lot to them," added Cavendish who made his Tour debut in 2008 before becoming world road race champion three years later.
As the peloton swept through the lush Rhone valley on stage five with vineyards and pretty villages skirting the river his Astana team hogged the front right of the peloton as light rain fell.
A long home straight in the tiny village of Saint-Vulbas helped them form a lead out train the 'Manx Missile' mastered after an early mix up and he powered across the finish line well ahead of Belgian Jasper Philipsen, last year's sprint points green jersey winner.
"We didn't nail it as a team like we wanted to do," Cavendish insisted.
"But the boys improvised and got me there in the best position," he added.
After celebrating with several of his children on the podium with his wife in the crowd Cavendish was in an exhausted mood.
"I love this race, I love it when I ride on it," he told a packed out press conference.
"I love it when I watch it and I'll try and continue to do that," he added having also won stages on the Giro d'Italia and the Vuelta a Espana.
Given that Cavendish was vomiting in the saddle and struggling to keep up on the opening day of this year's Tour, the feat is all the more remarkable.
"I was seeing stars it hurt that much," he said after stage one between Florence and Rimini in sizzling heat.
On paper stage three also suited him but he suffered a mechanical problem to his bike in the closing kilometres
Pogacar's love for Cavendish
Race leader and two-time former winner Tadej Pogacar almost hit a traffic island, causing a wave of movement and a pile up of bikes and bodies behind him.
But the Slovenian preferred to focus on Cavendish after the race.
"I used to watch him on television and we loved him," Pogacar said.
"Just back there I saw him and he said hey, don't you go breaking my record," he jokingly added.
Pogacar is 25 years old and already has 12 stage wins.
He still leads the overall standings which he enjoyed with a full yellow kit while Belgian Remco Evenepoel remains second at 45sec with defending champion Jonas Vingegaard third at 50sec.
Biniam Girmay, who became the first black African to win a Tour stage in Turin on Sunday took the sprint points green jersey on Wednesday after coming ninth in Saint-Vulbas.
Cavendish took a moment to congratulate the Eritrean sprinter who is 15 years his junior.
"Biniam set a record in Turin and now I've set one here," he said.
"So much goes into this and even one stage can make your career," he added.
In 2023 Cavendish left the Tour in an ambulance after a banal crash bamboozled his plans.
Two seasons previously when Cavendish equalled Merckx's stage haul in Carcassonne, it was his fourth win on that edition racing for Quick Step after years in the wilderness suffering from Epstein Barr virus.
He missed out on a 35th stage on the Champs Elysees coming second and then missed the cut for the 2022 Tour as Quick Step picked Fabio Jakobsen 10 years his junior.
Cavendish joined Astana in 2023 before being persuaded to sign a one-year contract extension for this season having considered retiring.
Thursday's 163.5km racing between Macon and Dijon, in the Burgundy wine-growing region, will be another day for the sprinters.
