Tencent Holdings, China's biggest social network and gaming company, was a great partner, Cook said, adding that he thought very highly of its founder, Pony Ma.
Apple's shares were little changed on Wednesday morning after Apple CEO Tim Cook discussed Apple's performance in a speech in China.
As reported by the Washington Post, "The World Internet Conference held in the eastern Chinese city of Wuzhen is meant to promote China's vision of "cyber-sovereignty" - the idea that governments all over the world should have the right to control what appears on the Internet in their countries".
Apple received criticism for pulling virtual private network and messaging apps from the Chinese store due to pressure from the country's regulators.
Yet Cook expressed confidence that some of the apps will eventually be reinstated, according to reports from Reuters.
"My hope over time is that some of the things, the couple of things that's [sic] been pulled, come back. I have great hope on that and great optimism on that", Cook said, adding he always tried to find ways to work together and if he was criticised for that, so be it.
China is the company's third-largest region by sales, though recently it has lost some market share to high-end handsets from local rivals.
"We have been notified by the Ministry of Public Security that a number of voice over internet protocol apps do not comply with local law, therefore these apps have been removed from the App Store in China", an Apple spokeswoman said at the time, according to Reuters. The companies have since reconciled their differences.
Earlier this year, Apple said that developers had earned roughly $70 billion (£52 billion) in total revenue through the store. Netizens had previously been using VPN apps to bypass China's internet restrictions.