Despite losing his right eye in an altercation with another sea bird, Captain is considered a good dad to son Dave and shares a burrow with fellow penguin Flip.
As a result of his eye injury, he must be fed from his left side and wouldn't survive in his natural wild habitat.
He is also considered one of the aquarium's nicest penguins and described as a "real gentleman".
National Aquarium of New Zealand keeper Amy Giddens said she backed Mo to take this year's title.
"There are a lot of Mo followers online, and he definitely received a large number of votes, however I think Captain's efforts in renovating his burrow recently and generally being a good penguin had touched people's hearts," she said.
"I'm sure there will be some interesting comments from fans of Mo coming through our social media channels in the next few days."
More than 15,000 votes were cast throughout the 2020 competition, setting a new record – with votes cast in New Zealand, USA, UK, Australia, Turkey, Costa Rica, Estonia, Trinidad and Tobago and Venezuela.
The aquarium team also noticed a large spike in votes from Vietnam over the past couple of days.
"This is a way to educate our followers, and people across New Zealand and the world about the challenges little penguins and other wildlife face, and how we can help protect them," Giddens said.
"Sharing the stories of our little penguins and how they came to live at the National Aquarium creates a greater understanding about conservation."
All of the penguins at the National Aquarium of New Zealand need help from specialist staff after either being abandoned as chicks, injured in dog attacks or becoming sick in the wild.
The facility is a rehabilitation centre for little penguins, assisting with recovery and returning them to the wild. Some penguins are not strong enough to return to their natural habitats, so they find a permanent home at the aquarium.