It is the second sizeable donation the couple - who won £161m on the Euromillions in 2011 - have pledged to the Firhill club.
They put up £750,000 to set up the Thistle Weir Youth Academy.
"The Thistle Weir Youth Academy is absolutely massive for this club," said Thistle chairman David Beattie.
"We are grateful to Chris and Colin for this further generous donation."
The latest investment will fund the academy operation for the next five years.
"The development across the Thistle Weir Youth Academy in recent years has been nothing short of phenomenal," Beattie continued.
"Youth development is a massive part of the club's long-term future and is something that the club sees as essential to underpinning further success.
"Although a long-term project, we are already starting to reap the rewards from the initial investment as players break through to the first team.
"Huge credit has to go to Gerry Britton (academy director) and Scott Allison (head of academy coaching), along with their dedicated team, for building that infrastructure from virtually nothing."
Partick Thistle have received £500,000 towards their youth academy from lottery winners Colin and Christine Weir.