What worked for me? Don't know because it was an accumulation of things. Here's the chronology.
Sight singing in high school. Playing tunes by ear (also in HS). Sight-singing and ear training, systematically in college and with added concentration on chord progressions. More playing by ear, this time including playing along with recordings. Gradual eye-ear association by conducting and also transcribing. Eventually, I got to a point where I could sight-sing and take dictation of atonal music.
Sorry, I can't break it down for you.