The Sunweb rider forced a selection with 30 kilometres to go and later went solo to take the race win after finishing second in 2017.
Kragh Andersen said: "I really wanted this win, but I didn't believe it was possible. I was really focused on today so I'm super happy with the outcome," Kragh Andersen said.
He finished 25 seconds ahead of Niki Terpstra (Quick-Step Floors) and Benoit Cosnefroy (AG2R) after dropping both with 11 kilometres to go on a course which was changed to favour classics and cobbled specialists from one better suited to sprinters.
"The parcours were awesome, I loved it," Kragh Andersen said. "It's my first classic-style win and I couldn't be happier. I didn't stop to enjoy it until 100 metres to go, the last 10 kilometres were super hard but it was completely worth it.
"The kind of guys I've beat here is really awesome and I'm surprised I was able to do it. It really is the best of the best here so this win is crazy."
A five-man breakaway went clear at the start of the race, consisting of Dries de Bondt (Veranda’s Willems-Crelan), Bernhard Eisel (Dimension Data), Thibault Guemalec (Fortuneo-Samsic), Emiel Vermeulen (Roubaix Lille Metropole), Brian Van Goethem (Roompot-Nederlandse Loterij) and
In his last race as a professional Sylvain Chavanel ((Direct Energie) was in the early eight-man break which fell apart once the race hit the first of the nine gravel sections.
As the gravel and hills took their toll on the bunch, Terpstra and Kragh Andersen later found themselves paired at the head of the race before they were joined by a Cosnefroy who bridged across from the chasers.
The trio maintained their tempo to the point where Kragh Andersen made his move to take control of the race.