Pertwee credited his performance as the Third Doctor for helping him work out exactly who he really was when he was not resorting to comedic disguises or voices: a dapper, technologically oriented man of action. This was because Terrance Dicks had advised him to act out the Third Doctor as himself: in effect, to "play Jon Pertwee." Pertwee remembered asking himself, when so advised, "Now who is that?" His performances, he said in his later years, helped him to determine the answer to that question.
He had one of his most memorable film roles in the Amicus horror compendium The House That Dripped Blood (1971). Filming in the summer of 1970, between his first and second Doctor Who seasons, Pertwee played the lead in the last segment of the film as Paul Henderson, an arrogant horror film star who meets his doom thanks to a genuine vampire cloak.
In 1973, during the peak of his Doctor Who powers, Pertwee endorsed the Co-op's Baking Your Cake and Eating it, a recipe book written by Sarah Charles. It has been given the unofficial title of The Jon Pertwee Recipe Book.
In early 1974, Pertwee announced he would step down as the Doctor to resume his stage career in The Bedwinner, also citing typecasting in the role as the reason for leaving, though later he would say that the catalyst for his departure was the death of his good friend and co-star Roger Delgado (The Master) and the departures of co-star Katy Manning and producer Barry Letts. His last full-time appearance in the series was in the story Planet of the Spiders in June 1974, which finished with Tom Baker replacing him in the role. Although ratings for the series rose higher under his successor, who overtook him in popularity and became widely viewed as the definitive Doctor, Pertwee's tenure in Doctor Who has been praised by The Daily Telegraph critic Dr. Tim Stanley as "the high point of the programme as a serious piece of science-fiction".
Pertwee later reprised the role in the 20th anniversary story The Five Doctors and the Children in Need story Dimensions in Time, in two radio adventures and on stage in Doctor Who – The Ultimate Adventure. On 14 April 1971, Pertwee was the subject of Thames Television's This Is Your Life.