Having won the 2005 World title and 2008 UK crown, Murphy stays on course for a career 'triple crown', after making two breaks of 103 to advance.
He will meet Mark Allen who beat Joe Perry 6-4 earlier in the day.
"For long periods of that match, it was embarrassing," Allen told BBC Sport. "I just could not get anything going.
"I was delivering the cue so badly."
Allen went 3-1 ahead, before England's Perry made breaks of 50, 68 and 67 to make it 4-4. But Northern Irishman Allen made a break of 55 and then clinched the 10th to progress.
Allen went through into his second Masters semi-final but will have to improve significantly if he is to trouble Murphy.
Scotland's Maguire opened with breaks of 137 and 67, before Murphy responded with 103 as he levelled at 2-2.
Some superb potting allowed Englishman Murphy to go ahead in the match for the first time at 4-3, and another century plus the 10th frame gave him victory.
Shaun Murphy reached his third Masters semi-final after an enthralling 6-4 victory over Stephen Maguire at Alexandra Palace.