Cooper is no stranger to winning at this level. The Mount Maunganui man has won motocross titles in Australia and New Zealand.
He won the MX1 (450cc) class in Taupo in 2011 and last season.
His dominance this season was impressive once again - he won nine of the series' 12 races and finished no lower than third in the other outings.
He started the day a huge 37 points ahead of Scottish visitor Billy MacKenzie (Yamaha) and, after finishing 1-1-3 in Taupo on Saturday, he was able to extend his advantage to 51 points at the conclusion of the championship.
Taupo's Brad Groombridge (Suzuki) took third spot on the podium, just one point further back from MacKenzie.
Rotorua's Michael Phillips finished in fourth.
Meanwhile, in the MX2 (250cc) class, Mangakino's Lamont realised a career-long dream of winning a senior national title.
Interestingly, he had been on the operating table at Rotorua Hospital on Thursday night having his appendix removed and it was a heavily-strapped and bandaged Lamont who lined up to race at Taupo just two days later.
Despite the surgery, Lamont won the MX2 title with a race left to run on Saturday and, in substantial pain, he opted out of the series' final MX2 race. He still finished the championship 11 points ahead of Dargaville's Hamish Dobbyn (KTM).
Meanwhile, in the 125cc class, two reigning national junior champions dominated the series.
Hamilton's young rider Josiah Natzke led by a healthy 35-point margin at the start of racing at Taupo and soon extended that to 74 points by the end of the afternoon.
He won his first senior title ahead of Hadleigh Knight, of Atiamuri.
Final standings for the 2014 New Zealand Motocross Championships:
MX1 (450cc) class:
1 Cody Cooper (Mount Maunganui, Honda) 287 points, 2 Billy MacKenzie (Scotland, Yamaha) 236, 3 Brad Groombridge (Taupo, Suzuki) 235.
MX2 (250cc) class:
1 Kayne Lamont (Mangakino, Husqvarna) 254, 2 Hamish Dobbyn (Dargaville, KTM) 243, 3 Jay Wilson (Australia, Yamaha) 216.
125cc class:
1 Josiah Natzke (Hamilton, KTM) 289, 2 Hadleigh Knight (Atiamuri, KTM) 215, 3 Logan Blackburn (Te Puke, Yamaha) 190.