Spain's world champion Jorge Lorenzo, on the works Yamaha, qualified fifth with Honda's Dani Pedrosa fourth.
Crutchlow grabbed the top slot with a record qualifying lap time of one minute 55.527 seconds and he could say he had done it with all of the top riders present. Lorenzo was absent for the Dutch round.
"It is going to be a long, tough race tomorrow," the Briton, who is switching to Ducati next season, told the BBC.
"In all honesty the last couple of races haven't gone to plan... but everyone seems to be struggling a bit and we seem to be getting there slowly," he added.
Crutchlow had been unhappy after Friday's practice with a new fuel tank fitted to his bike but was fastest in Saturday practice.
(Reporting by Alan Baldwin in Spa-Francorchamps, editing by Josh Reich)
