TRENTON, N.J. – Baseball is a game of adjustments, something highly regarded Boston pitching prospect Matt Barnes understands well.

Barnes, the No. 3 overall prospect and top pitcher in Boston’s farm system who tore through Single-A last season, made his fourth start at the Double-A level and took the loss in Portland’s 6-3 defeat at Trenton on Friday night.

The 6-foot-4 righty, who was picked by the Red Sox in the first round of the 2011 draft, showed flashes of the pitcher who overpowered hitters last season between stints at Salem and Greenville. But he also stumbled at other times against the hard-hitting and talented Thunder lineup.

Barnes (1-1) allowed six runs on 11 hits, including six extra-base hits, in 42/3 innings as his ERA rose to 9.00. Relying on a four-seam fastball that consistently clocked in the low-90s, Barnes struck out six batters — five of whom went down swinging.

“I felt pretty good, they put some good swings on the ball,” Barnes said. “Obviously it’s not what I wanted in terms of statistical numbers, but you have to take away the positives and build on the positives.”

The pluses were a fastball with good velocity and a change-up that he felt comfortable throwing. Barnes’ third pitch, the curveball, still is a work in progress, as is finding consistency with his bread-and-butter fastball.

“He threw some with quality,” Sea Dogs Manager Kevin Boles said. “It looked like he couldn’t sustain anything as far as being consistent. He threw some pitches down and he elevated a couple. And with this lineup, they have a lot of weapons.”

Barnes’ first inning was a capsule of his evening, as a triple by Jose Pirela and an RBI double by J.R. Murphy were sandwiched between three strikeouts.

A pair of doubles in the third, including a two-run double to left by Kyle Roller, gave the hosts a 3-1 lead. Trenton tacked on two more runs in the fourth and another in the fifth when Barnes exited after 83 pitches, 53 of which were strikes.

Through four starts, the native of Bethel, Conn., has allowed 14 runs on 23 hits in 14 innings. That’s a change from the shutdown pitcher who opened eyes last season at Greenville and Salem, when he combined to go 7-5 with a 2.86 ERA with 113 strikeouts in 1192/3 innings.

“This year I’m facing 23-, 24-year-old guys who’ve been playing for a while,” Barnes said. “Last year it was 18-year-old kids right out of high school or international players. It’s completely different.

Boles is confident Barnes will make the necessary changes to succeed at this level in his second season of pro ball.

“He’s a guy we think very highly of and (he’s got) a three-pitch mix,” Boles said.

“He has a lot of good stuff and a lot of good qualities. From the limited look we’ve seen of him, we’re excited about Matt Barnes.”