The Red Bull driver made the best of the very limited running on offer, emerging from the garage on the intermediate tyres at just the right time to end up 1.5s clear of Williams drivers Felipe Massa and Lance Stroll.
It took more than 45 minutes for the session to properly get going, thanks to a lengthy red flag.
The stoppage was initially called shortly after the session had started, due to weather conditions in Shanghai being unsuitable for the medical helicopter to land at the hospital if needed.
It wasn't until 47 minutes after the session started that the track went green again.
While not actually raining the circuit was still wet, the majority of drivers appearing on wets before quickly switching to intermediates.
The changeover proved a little tricky for the Haas drivers, both Kevin Magnussen and Romain Grosjean spinning on the intermediates.
It was Lance Stroll that set the first step forwards on the inters, moving from a 1m54.508s to a 1m52.507s to go fastest.
Verstappen then proved beyond doubt that the intermediate was the best tyre, moving ahead of Stroll with a 1m52.266s before immediately improving to a 1m50.491s.
That wound up being the best time of the session. With half an hour to go a virtual safety car was called while crews retrieved Nico Hulkenberg's beached Renault from the Turn 3 gravel trap after a spin.
By the time that was cleared, the red flag was back out as conditions grounded the medical helicopter again. With four minutes to run, and no sign of improvement in the weather, the session was called off.
Verstappen ended up 1.5s clear of the two Williams cars, with Grosjean splitting Toro Rosso drivers Carlos Sainz and Daniil Kvyat behind the top three.
Fernando Alonso was the last of the drivers in the 1m53s in seventh, with Daniel Ricciardo down in eighth, 3.5s slower than his team-mate, having been one of the few drivers to stay out under VSC conditions in the hope of getting some more meaningful running.
The premature end to the session meant none of the Mercedes or Ferrari drivers were anywhere near the front of the field. Valtteri Bottas did the most running of the 'big four', just four laps on the wet tyres leaving him ninth in the times.
Lewis Hamilton didn't set a time, having been strapped in ready for a run right as the second red flag was called.
It was a similar story for Ferrari drivers Sebastian Vettel and Kimi Raikkonen, neither setting a time.
China GP Free Practice 1
|1||Max Verstappen||Red Bull/Renault||1m50.491s||-||4|
|4||Carlos Sainz||Toro Rosso/Renault||1m52.840s||2.349s||5|
|6||Daniil Kvyat||Toro Rosso/Renault||1m53.314s||2.823s||4|
|8||Daniel Ricciardo||Red Bull/Renault||1m54.038s||3.547s||7|
|18||Esteban Ocon||Force India/Mercedes||-||-||2|
|19||Sergio Perez||Force India/Mercedes||-||-||3|