Japan's former Masters champ recorded two eagles, five birdies and one bogey in his eight-under round to leave him at 12 under for the tournament, one stroke clear of Ryder Cup-bound Justin Rose, Sweden's Ludvig Aberg and Norwegian Viktor Hovlund on a quality-packed leaderboard.
Rory McIlroy's charge through the back nine included him escaping the threat of missing the cut, but untidy play continued to plague him as he carded a level-par 72 to end the day on three under, nine shots behind Matsuyama.
The Australian challenge was being spearheaded by Elvis Smylie, who shot a four-under 68, and veteran Adam Scott, who went round in 69, as they were both handily placed at five under for the tournament, just outside the top 20.
Between them, they didn't drop a shot on Friday (Saturday AEST), while Min Woo Lee is certainly not out of it either at four under despite his disappointing second-round of 73.
Rose and Hovlund - the latter eagled the 18th for the second day running - followed their opening-round 67s with 66s, while Aberg carded a 69 after bogeying the 17th.
Matsuyama was thrilled with his double-eagle round. "Obviously I would like to achieve something really big here. But the conditions are going to be changing and hopefully I can adjust to that. I'm looking forward to the weekend."
There were 11 members of the Europe team playing in their final tournament before the Ryder Cup in New York and only one failed to make the cut — rookie Rasmus Hojgaard, who was five over after a 75.
Hovland said he couldn't remember chipping and putting as well as he did, as he made three straight birdies from the fourth, birdied No.16 and holed a 40-foot putt for eagle at the last.
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