Todd Haynes needed to get approval from Bob Dylan to use his music, since (unlike in his Velvet Goldmine (1998) where David Bowie did not give his permission for his music) he felt the film would not work without it. At the encouragement of Dylan's manager, Haynes wrote a one-page summary of his concept and the characters, which Dylan approved. It took another 6 years to get the film made due to funding difficulties.
Different sections of the film were inspired by different cinematic sources. The "Jude" section was inspired by 8½ (1963), the "Billy" section was inspired by the so-called "hippie westerns" of the late 60s and early 70s (such as Sam Peckinpah's films) and the "Robbie" section was inspired by the films of Jean-Luc Godard, especially Masculin Féminin (1966).
Todd Haynes noted that when he got his favorite actor and actress, Christian Bale and Julianne Moore, together to shoot the still photographs early on in the film, how different their acting styles were. Moore kept joking and laughing with Haynes and only a few photos could be used where she had a straight face, while in every shot the more method-based Bale appeared serious and intense.
The man in the viking outfit and café Wha? seen in the beginning sequence of the film are all references to Bob Dylan's first experiences playing music in New York city. The man in the viking outfit was Moondog, a blind poet Bob Dylan was associated with, and café wha? was where Dylan began playing music in New York. All of this information is shared in Dylan's book "Chronicles volume I".
In the "Jude" storyline, when Jude Quinn is revealed to have originally been Aaron Jacob Edlestein in high school, the picture shows Christian Bale although the "Dylan" in this storyline is played by Cate Blanchett.