I'm going to assume standard battle assumptions and that this is just Base Captain Marvel.
Doflamingo's advantages: Durability and AP (645+GT scaling to threads vs 615+GT), Speed (Mach 940+ vs Mach 247), hax via Parasito, Duplication via Black Knight, Transmutation of the battlefield via Awakening, Statistics Amplification via Busoshoku Haki, Combative intelligence (Manipulator/Deceiver vs a brute), Lifting Strength (this is almost not even worth mentioning), superior Precognition (Less random than Marvel's, but it also grants him 360 degree field vision to an unknown range)
Captain Marvel's Advantages: Energy Absorption (Could work vs Haoshoku Haki, if Doflamingo uses it), superior flight, Molecular Manipulation (How this works and at what level, I am unsure)
Both have some level of Regenerationn, and due to Marvel's stamina and range not being stated, I can't comment on that. Doflamingo will be doomed if he falls into deep waters, but that may not even factor.
Doflamingo clearly has a lot more versatility + advantages against Marvel, and Marvel's Energy Absorption is not really going to matter in this match-up if Doflamingo uses it once and sees first-hand that it's back-lashing.
Going by their profiles alone, I think Doflamingo has this simply due to having a larger array of abilities on top of slightly superior AP/Dura + his intelligence being more helpful in live combat compared to Marvel's. He's also much faster than her.
If there is something that I need to know about Captain Marvel, inform me.