The 27-year-old, who won in Prague two years ago, triumphed in 6.61 seconds with Theo Etienne and Andrew Robertson also qualifying for the semi-finals as second and third fastest.
Asha Philip also won her heat in the women's 60 metres during the morning session but now must wait until Sunday afternoon to compete for a shot at the final.
Kilty, Etienne and Robertson will wrap up on Saturday evening and Kilty believes he can go faster at the Kombank Arena in Belgrade.
He said: "It was a slow start, but I put my foot on the gas for 20m and then eased off - there's definitely at least another tenth I can take off.
"With the adrenaline my reactions will get quicker; now I'll relax before later, but I loved it out there."
Etienne won in 6.62 seconds with Robertson winning his heat in 6.66 seconds to complete a clean sweep ahead of Saturday's afternoon's semi finals.
"I'm as confident as I ever have been, but I just have to treat the rounds like any other race - we're all here for a reason, and I just want to perform and show everyone that I deserve to be here," said Etienne.
Robertson added: "I didn't get out well at all. At the finish I slowed it down a little too, but I think I definitely missed about a tenth due to my start - I was left in the blocks big time. I'm really happy generally though."
Philip won in 7.25 seconds, the fifth fastest time, and is hunting a first senior individual medal after success in the relays.
The 26-year-old, who won bronze in the 4x100 metres relay at the Rio Olympics, said: "I saw the German girl (Alexandra Burghardt) went full tilt in heat one, so I thought 'Okay, I don't want to kill myself out there', but obviously I knew I wanted to win the heat, so I just pushed on.
"I knew she (Lisa Mayer, German who finished second) was coming for me but I got out well. There are still things to work on - maybe I relaxed a little - but now it's about trying to qualify for the final."
Laura Muir will look to complete the first of her double when she races in the 1,500 metres final on Saturday evening before Sunday's 3,000 metres final.
She said: "It's hard to tell (about the standard of her competition) they'll be fresher than I will be because I'm running more than anyone else but I know I'll be very strong. I'm just going to bring my 'A' game and hopefully that'll be enough."
Lorraine Ugen and Jazmin Sawyers qualified for Sunday's long jump final, with Ugen passing the automatic standard of 6.60m with her first leap of 6.80m.
Ugen said: "I'm very happy - that's probably the easiest 6.80m I've ever jumped in my life. It felt really comfortable and I think there is more in the tank for tomorrow. I know that I'll have to jump something outrageous to win, but that's the aim, and I'll come out firing."
Sawyers, who jumped 6.54m to go through, added: "I'm into the final, and that's the whole point of today. I'd love to stop scraping through to finals - that really seems to be my style at the moment, and I'm not into it - but it's job done."