Miller (29) won the 43km-long ride in 2hr 17min 46sec from Mark Williams (Queenstown) in 2hr 18min 11sec, John Metzger (Wanaka) in 2hr 27min 53sec and Tim Rush (Oamaru) in 2hr 30min 05sec.
Miller was a novice mountain biker when he finished ninth in the event two years ago.
But he has built up stamina since that time and was fourth in the Australian 100km last year.
Miller had a 10sec cushion over Williams at the top of the last of the course's three big hills and put his foot on the accelerator across the top and won by 25secWilliams (37) is also experienced and finished seventh at the world 24-hour race in Canberra in October.
He worked together with Miller after they gained an early break to put distance between the pair and the rest of the field.
Metzger (33) has specialised in off-the-road triathlons for the past seven years and rode a steady race for third.
Tim Rush (Oamaru) emerged out of the bunch to claim fourth place.
Rush's father, David, a former New Zealand 5000m champion on the running track, easily won the short-course 23km mountain bike race in 1hr 23min 05sec.
He was followed home by Robert Stout (Dunedin) in 1hr 32min 15sec and Warwick McLaren (Dunedin) in 1hr 38min 01sec.
Hannah Thorne (34), of Dunedin, finished seventh overall on the long-course race and won the open women's title in 2hr 54min 45sec.
She was 7min ahead of Sharon Prutton (Christchurch), who won the masters women's title in 3hr 01min 26sec.
The third female home was Karina Dollman (38).
Erin Greene (Dunedin), the pre-race favourite, was forced to withdraw because of a torn calf muscle.
The open women's short-course race was won by Susie Burrows (Tapanui) in 1hr 59min 51sec from Amanda Hayward (Queenstown) in 2hr 04min 29sec and Merrin Brewster (Dunedin) in 2hr 09min 12sec.
