The young Addicks side took a first-half lead, before Blues forward Wes McDonald (pictured) levelled the scores with a 50th minute finish.
McDonald cut inside from the left of the box before firing home an unstoppable shot which flew into the bottom corner of the net.
But Blues were no match for their hosts, as they hit a further three goals with reply to seal a comfortable 4-1 home victory.
Blues academy coach Steve Spooner, admitted the better side won on the day.
“We started off very well and enjoyed some good periods with the ball, but we didn’t work their goalkeeper enough,” he said.
“But after 15 or 20 minutes, Charlton were far superior to us. Our players looked very tired and drained against a strong and physical Charlton side with very good technical players.
“After we’d levelled the scores we made a mistake to let them in for a second goal and then they had us on the ropes and scored two more. In the end, Charlton were well-worthy of the victory.”