The 25-year-old netted a double in Germany's 4-0 win over North Macedonia on Monday night, securing their place at the 2022 World Cup.
Flick only recently replaced long-time manager Joachim Low, and his impact on the squad has impressed Werner.
"He's very good for me. If a coach likes you and relies on you, it helps every player," said Werner.
"As a striker, I especially need to be trusted externally. I'm trying to pay it back and I hope that I can keep giving it back."
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