He had a car = simple past tense... 'He had a blue car when he lived in London.'
He had had a car = past perfect tense - 'He had had a car all of his life and was struggling to adjust to having to catch the bus everywhere after being banned from driving.'
Simple past tense = used to describe one completed event in the past.
Past perfect tense = used to describe two or more completed events in the past where one of the two events was further back in time than the other..usually the two are related. The form is that the past perfect tense should be used to describe the event furthest in the past and then the simple past is used for the more recent event.