They are both correct, but "Milyen ez az autó?" means "What is this car like?"

The subject in the original sentence is asking about the classification of the car in question, such as its kind/type/brand, while your sentence is more like a question about its general quality.

• What kind/sort of car is this? = "Milyen/miféle autó ez?"
• What kind/sort of car has a two-stroke engine? = "Milyen/miféle autónak van kétütemű motorja?"

Milyen fajta (kind) autó ez

You can use "Milyen autó ez?" or "Ez milyen autó?", but the one you said is not correct. "Milyen" and "autó" can't be separated by an other word.