Cooper (16), riding for Team Pink Pilates, won the race in 1hr 48min 43sec, bettering Roy's record of 1hr 57min 47sec set in 2008.
Followers have been keeping a close eye on the talented teenager after he came second to Roy last year.
"Last year it was Marcus and I the whole way," Cooper said.
"This time I decided to go nice and early up that first hill and held it off across the middle bit and then down the hill to the finish ... basically, this year I rode it all solo."
The Christchurch Boys' High School pupil is the youngest winner of any Motatapu event and has had a stellar season.
The 47km course traverses three high country stations from Glendhu Bay, Wanaka, through the Motatapu, Soho and Glencoe stations, finishing in Arrowtown.
Iconic Adventures director Geoff Matthews said 3200 riders competed in the mountain bike event, with Kath Kelly winning the female title for the second consecutive year in 2hr 20min 50sec.
Christchurch's Vajin Armstrong won the 42.2km off-road marathon in 2hr 51min 41sec, having edged out Jason Cameron, who was with him for the first 12km.
First time Motatapu entrant Sarah Coughlan, of Queenstown, was the first female across the line in the marathon, narrowly beating the course record of 3min 19min 56sec set by Melissa Moon, with a provisional time of 3min 19min 48sec.
Many of those competing in Saturday's events were racing in support of Christchurch.
Among those were Finance Minister and deputy Prime Minister Bill English; Christchurch-based multisport athlete Steve Gurney; and Olympic gold medallist Hamish Carter, all competing in the mountain bike; Dame Susan Devoy, who walked the 42.2km marathon in support of her Wonder Walkers initiative; and Team Pink Pilates, funding New Zealand women recovering from breast cancer through the Pink Pilates programme, with 100% of money raised over the weekend going to Canterbury women; and Air New Zealand chief executive Rob Fyfe, who ran the marathon to train for his upcoming Everest Base Camp expedition.
