Yann Kermorgant's early strike put Charlton in front but McNaughton's measured finish ensured a share of the spoils.
Both sides came into the game in poor form, with Wanderers losing three of their previous four fixtures whilst the Addicks only had tasted one victory in their last seven.
Dougie Freedman made one change to his Trotters line-up which lost 3-2 at Wigan last Sunday, with Chris Eagles coming back into the side to replace Darren Pratley.
Meanwhile, Chris Powell made three changes to the side that lost to Derby. Chris Solly, Richard Wood and Simon Church replaced Dorian Dervite, Danny Green and Bradley Pritchard.
It was a sluggish start from the home side and the visitors took advantage.
Kermorgant put in a low drilled shot from outside the box, which was only just scooped around the post by Andrew Lonergan. Moments after the resulting corner, Kermorgant then opened the scoring.
Rhoys Wiggins fired a ball low into the penalty area, which Kermorgant curled into the net from close range.
Wanderers were then caught napping again and could have easily been two goals down. Cameron Stewart's cross towards the back post found Lawrie Wilson on his own with plenty of time but despite there being no defensive pressure forthcoming, Wilson hit the ball horribly wide from six yards out.
It was Eagles who sparked the Trotters into life, as he ran through a clutch of Charlton defenders on his own and then forced a smart save from Ben Alnwick.
Eagles then almost got the assist for the first goal, but Lee Chung-yong's header from his cross was cleared off the line by Wood.
Lee was then in on goal again as Andre Moritz produced a sublime chipped pass to send the South Korea international through but he could not connect well enough to beat Alnwick.
Alnwick was keeping the Addicks in front as he made another great stop after a slick passing move between Eagles and Lee saw Joe Mason flick the ball towards the goal.
But the former Spurs keeper was helpless when Eagles found McNaughton free in the box. The on-loan Cardiff defender then steadied himself before he cut back on to his right foot and placed the ball into the top right corner for the equaliser.
The momentum was clearly now with Bolton and another magnificent one-handed save from Alnwick denied Mason again this time to make sure they did not go behind.
However, just as Wanderers looked to be in control, Charlton almost re-took the lead when Wiggins' volley was tipped athletically over the bar by Lonergan.
The Trotters were the side who went for it at the end but, despite Jay Spearing going close with a long-range effort, both teams failed to get the winner.