Kevin Garratt was held in August 2014 and accused of stealing state secrets. His wife, Julia Garratt, was freed on bail in February the following year.
The couple had been living on the North Korea border before their arrest, where they said they were helping refugees.
His release follows Canadian Prime Minister Justin Trudeau's recent first official visit to China.
The Garratts' eldest son called the espionage allegations at the time "absurd".
A statement from the family said Mr Garratt was deported on Thursday following a ruling in the case.
"The Garratt family thanks everyone for their thoughts and prayers, and also thanks the many individuals who worked to secure Kevin's release," the statement said.
The Canadian prime minister said he was "delighted" by Mr Garratt's homecoming.
"We remain deeply impressed by the grace and resilience of the Garratt family," Mr Trudeau added.
In an August press conference, Chinese Premier Li Keqiang assured the Canadian PM that Mr Garratt would be treated humanely. Mr Li will meet Mr Trudeau next week when he makes an official visit to Canada.
The Vancouver couple had lived since 1984 in Dandong, China, where they ran a popular coffee shop and carried out Christian aid work.
The Chinese government had denied accusations the couple's arrest was retaliation for the detention of a Chinese man in Canada who had been wanted in the US for allegedly stealing fighter jet documents.