The president-elect will also name Lisa Jackson, former head of the New Jersey Department of Environmental Protection, to head the EPA.
Meanwhile, Nancy Sutley, a deputy mayor of Los Angeles for energy and environment, will head the White House Council on Environmental Quality, the newspapers said.
The three appointments are expected to be announced by Obama later this week, the reports said.
Chu, who is director of the Lawrence Berkeley National Laboratory, won the Nobel prize for physics in 1997 for his work on the "development of methods to cool and trap atoms with laser light."
In his current role, his work has focused on climate change.
Environmental groups have said that Obama's apparent choice shows that the president-elect is keen to implement renewable energy technologies in an attempt to reduce carbon emissions.
"It's a great sign to see a scientist named as head of this very important department, because it sends a signal that the issues of climate change and energy go well beyond ideology," Keya Chatterjee, from the World Wildlife Fund, told Al Jazeera.
"Our hope is that his first task we be how as a society in the US can achieve a low-carbon economy ... at a pace that matches the urgency of the problem [of climate change]."
Obama is also expected to name Tom Daschle, a former US senate majority leader, as his choice for health and human services secretary on Thursday, a Democrat official said.
"He will be the White House's voice on this critical issue" of health care, said the official, who is not allowed to speak publicly about the nomination.
Should he be confirmed, Daschle's work will focus on pushing changes to the US' health care legislation through the Democrat-led congress.
Daschle will also head the new White House Office of Health Reform, while the deputy director in that office will be Jeanne Lambew, who in the past has worked with Daschle on investigating health policy.