The European Union opened the world's largest cap-and-trade scheme for greenhouse gases in 2005 and California is aiming to open the second-largest next year.
"How can we take care that we are not building isolated systems, but linkable systems?" Hedegaard asked, describing a theme of her meeting with Brown.
Countries such as China, South Korea and New Zealand were already trading carbon, or planning to, she said.
The Californian carbon market had been due to begin on 1 January 2012 but on 18 March, environmentalists won a court order that could delay it.
The Association of Irritated Residents (AIR) will now draft a detailed order outlining their case that the proposed regulations will allow the state's highest polluting industries to continue or even increase pollution.
They claim that alternatives to a carbon market have not been properly considered. The state of California will appeal the court order.
But Commissioner Hedgaard focused on the importance of integrating different cap-and-trade schemes.
"Each country might want some special ways of doing it, but of course it's also practical that whatever we do in each different region can be linked, so that in the end we sort of have this vision of having a global price on carbon," she explained.
Experts from Europe and California are now expected to begin drafting more specific plans.
Governor Brown's office did not comment immediately on the meeting.
(EurActiv with Reuters.)