Aitken (17), an Otago Boys High School pupil, won 10 gold medals: five in athletics and five in swimming at the championships in Christchurch.
It was Aitken's fourth Independence Games and he displayed experience and maturity to help his younger team-mates perform at their best.
The Otago team of 11 won the teams event for the first time.
"It was special for me to win the top male trophy and to help Otago win the teams event as well," Aitken said.
Aitken's gold medals came in the 100m (15.50sec), 200m (31.50sec), 600m (2min 08sec), shot put (9.16m), discus (22.19m), 25m freestyle (24.38sec), 25m backstroke (29.82sec), 25m breaststroke (35.31sec), 50m backstroke (1min 07sec) and 50m breaststroke (1min 27sec).
Aitken is now the leading figure in sport for the disabled in Dunedin and sets an example with his dedicated approach to training.
Aitken is jointly coached by Jim Baird and Mike Weddell and his life revolves around training at the Caledonian Ground and competing in athletics and swimming.
The event was the 19th annual South Island Independence Games for children with intellectual and physical disabilities.
Shaun Markham (13), a pupil at Kings High School, continued his good form from the Otago secondary schools athletics championships in March.
He won five gold medals in Christchurch: in 100m (48sec), 200m (1min 52sec), starfish race in the pool (9.34sec), kickboard 10m (40.56sec) and back kick 10m (32sec).
Dunedin's Josh Weatherston (9) won six gold medals, Clyde's Jack Wellstead four, Rhys Walsh (Dunedin) three, Dunedin's Amy Roxburgh (4), amd Clyde's Jack Wellstead (10) four.
The other Dunedin gold medallists were Bradley Caffell (12), Haidee McRae (12) and Liam Monzari (13).
From the Waitaki team, Freyja Plumridge-Frew won seven gold medals, Jordan Simpson six, Ryan Algar six and Sheamus Neilson four.
The other gold medallists from Waitaki were Quentin Whalley, Emma Robb and Emma Anderson.
At a glance
> Gold medallists:
Amy Roxburgh, Bradley Caffell, Ella Fox, Haidee McRae, Jack Wellstead, Josh Weatherston, Liam Monzari, Matt Aitken, Rhys Walsh, Shaun Markham.
