"He was really good for me at Melbourne Heart," Thompson said. "He brought me to the club and in terms of coaching I thought he made a massive difference to my game.
"My first year under him was my best year in football.
"'JVS' is a great man-manager and he did wonders for my confidence. He showed a lot of faith in me. He pretty much said 'I rate you as a player and I want you in the side, so just do your thing'.
"He put me at stopper. It wasn't exactly a position I thought I was best suited in, because I'm not the tallest player, but he had confidence in me and I reacted well to that and did well in the position."
City goes to Suncorp Stadium to play Brisbane Roar on Friday night with a typically inconsistent record. So far this season it has gone draw, loss, win, loss, win loss and is in seventh place on the table.
Thompson, who played 221 games spread between Heart, Newcastle Jets and Sydney FC, said City had a strong team on paper and that it was up to the players to produce consistently good football.
"The players have got to go out there and perform. I mean, that's a given," Thompson said.
"The coach has got to have man-management skills and get those players wanting to play for him, but JVS has got that ability.
"His man-management when I was there at the old Heart was great, but the personnel wasn't necessarily good enough.
"People mention (Aaron) Mooy not being available when City lost last week and that they're a one-man band, but, while he's hard to replace, if they want to go further in the league as a team they're going to have to learn to perform when he's not there or he has a bad game.
"I like the way City look on paper. I love (Bruno) Fornaroli up front, I think he's unbelievable. I think Mooy is fantastic. I think once (David) Williams and (Corey) Gameiro get a bit of fitness they're going to be dynamite.
"There is some inexperience among the back four, though. The players there have great potential, but they need to start defending better as a unit."
Thompson said Van't Schip was tactically very good.
"When we played the better sides, we did well," he said. "The games we struggled in were the ones we should have won. That may have been a bit of complacency from the team, I don't know.
"We managed to beat Brisbane a number of times when they were at their peak, so he was clever in that way. They played a European style and it felt like home to JVS playing a side like that because he had seen it day in, day out and when we played them he knew how to go about it."
Thompson spent three seasons at Heart. In his last season, 2012-2013, he was coached by John Aloisi, who cut him from the squad at the end. Aloisi was himself sacked midway through the next season.
Aloisi is now experiencing a coaching revival in charge of Roar and Thompson said he was happy for him.
"It was a bitter feeling to have it end that way for me at the club but that's just football," he said.
"It would be easy for me to be negative about 'JA' because he let me go but I'm not the only person who has been let go by a club, so for me to do that would be stupid.
"I don't think of him like that at all. I disagreed with the decision, because I thought in a disappointing team season I was actually quite good as an individual but I don't have any hard feelings towards JA and I'm happy for him and what he's doing now.
"He had the disadvantage of being a bit inexperienced in his first year at Heart but he also had a few players who probably weren't willing to do it his way.
"He's got an older head now and a group of players who want to play his way."