The elite mountain biker from Christchurch won by 11sec from Jimmy Pollard, of Queenstown and Leighton Kirk, of Dunedin, was third.
Pollard was actually quicker in four of the five stages than Cooper but Cooper always had the race under control after a strong opening leg on Flagstaff.
Rosara Joseph was a more convincing winner in the women's race. The Olympian finished nearly three minutes clear of Natalie Jakobs, of Queenstown.
The race is made up of five stages over the two days and covers Mt Cargill, Signal Hill and Flagstaff. Riders do not know the exact routes until the day before racing starts.
About 200 riders entered the competition, which is in its third year.
Cooper said he had enjoyed the event and getting out in front early was the key.
''I think into the last stage I was ahead by about 21sec, so that was enough and I was reasonably relaxed,'' he said.
''But it was quite hard. It was quite slippery in places, so basically you just had to ride smooth.''
Cooper (20) is targeting a few cross-country races over summer, including the national championships in Rotorua early next year.
But his main focus for 2015 is to qualify for Olympic selection.
''I just need to get more consistency in my results. This is my third year on the circuit now and I think I have the speed but it is just about getting the consistency and just trying to put it all together.''
He hoped to cut back on his travelling next year and concentrate on racing more.
The thrilling win in Glasgow in August had given him some confidence, he said, and showed he had the speed to compete.
Competing at the 2016 Olympics at Rio de Janeiro was the short-term aim but racing at the Olympics in 2020 and 2024 were the main goals.
Joseph, of Wellington, graded as a masters athlete, was too quick for all the others, and successfully defended her title from last year.
She said it was a tough race and there was some good racing.
The 32-year-old was glad it did not rain yesterday morning, as she would have spent most of the time sliding down Signal Hill.
Defending men's champion Sam Nicholl was a late withdrawal from this year's event.
One competitor suffered a broken arm but apart from that all other entrants came through the two-day event well.
