The new design places a list of a user's friends on the right side, and the message content on the left.
According to the Daily Mail, some users have accused the firm of simply copying Apple's two-pane design.
The social network giant hopes it will attract more users to the service, and will make its system more reliable.
"A lot of thought and care went into this new version of messages, and we hope you'll like it," Facebook said in a statement.
"There's so much more we can do to make the world more open and connected, and to make our messaging system more reliable and more flexible," it added.
According to the paper, Facebook has also overhauled the way users can share pictures, and added emoticons in a bid to attract people to the service.