1. My father goes to work by car.

2. My father goes to work by his car.
3. My father goes to work in his car.

(Which one is grammatical?)

All three sentences are grammatically correct, but there are slight differences in meaning and usage.

1. "My father goes to work by car."
This sentence is a general statement that means your father goes to work using a car as a means of transportation. It does not specify whether it is his own car or someone else's car.

2. "My father goes to work by his car."
This sentence explicitly states that your father uses his own car to go to work. It emphasizes the ownership of the car.

3. "My father goes to work in his car."
This sentence also implies that your father uses his own car to go to work, but it additionally implies that he is physically present inside the car while traveling to work.

Overall, sentence 3 is the most commonly used and idiomatic way to express this idea. However, depending on the context and what you want to emphasize, any of these sentences can be used.

I would say "my father drives his car to work". 1 is probably the most acceptable of those choices though.