The former Nationals star didn't get specific or repeat what the hecklers were saying, but he wasn't happy following a 5-2 loss, the Phillies' fifth consecutive setback.
"They were fine all game, talking about myself and things like that," Harper said. "I get it everywhere I go. That's nothing new.
"But the last two innings, it's just not right. It's not right."
Harper said he was eager to get back to Philadelphia and the great fans there.
"I've got 60,000 fans up in Philly that appreciate me as a player, appreciate me as an individual and my family," Harper said. "I owe a lot to those people up there in Philly, because they show up for me every single night and they're there to cheer us on and boo us and keep us going as a team and as individuals, as well."
Harper left Washington after playing 927 games for the Nats over seven years, participating in six All-Star Games and winning the 2015 National League MVP Award. He has been a target of boos since signing a 13-year, $330 million contract with the rival Phillies.
Washington already has clinched an NL playoff spot.
In the teams' first matchup in April, the boos by Nationals fans started when Harper's name was announced in the lineup, and derisive shouting followed during a video montage of his biggest moments with the Nationals. Harper was then booed at every at-bat, and when he took his position in right field, several fans were wearing white shirts that spelled out T-R-A-I-T-O-R.
He got a bit of retribution during that contest five months ago with a 458-foot homer that he punctuated with a bat flip.
Harper acknowledged he heard the boos in April, saying: "For me, that's part of sports, part of the game."