Police said the suspects, aged 19, 23 and 24, were being held in relation to an incident that may be linked to the larger blaze on Saturday.
Fire services from across the county battled the fire using helicopter water drops to quell the flames, which is now believed to be under control.
More than 70 firefighters and 12 engines remained at the scene on Sunday.
The exact cause of the larger fire is still unknown, but grass and heather on moorland can easily dry out and ignite in hot weather.
The Met Office confirmed Saturday was the hottest day of the year so far, with the temperature reaching 25.5C in Gosport, Hampshire.
West Yorkshire Police said in a statement on Sunday afternoon: “We can confirm that three men have been arrested in connection with a fire on Ilkley Moor yesterday.
“The men, who are aged 19, 23 and 24, remain in custody at this time and enquiries are ongoing with the fire service to establish if this incident is linked to the larger blaze.
“The fire service is continuing to tackle the blaze and members of the public are advised to avoid the area.
“The blaze is believed to now be under control, but we would like to remind members of the public that this recent hot weather may have made some moorland areas tinder dry, which means that even small fires may spread rapidly in these conditions.”
“Awful scenes on Ilkley Moor and yet more reminders of why we urgently need to tackle climate change,” he wrote.
“Thanks to the firefighters on the front line working in such difficult conditions.”
Police and Bradford Council have warned the public to stay away from the areas while firefighting operations continue.
Agencies contributed to this report