Eisenstein's relationship with his parents, particularly his father, was strained. He later reflected on this estrangement as a formative experience that contributed to his rebellious and iconoclastic artistic sensibilities.

Eisenstein cultivated close friendships with intellectuals, artists, and writers, including the literary critic Viktor Shklovsky. These relationships provided him with intellectual stimulation and emotional support throughout his career.

Eisenstein's sexuality has been the subject of much speculation. While he never publicly identified as gay, many scholars believe that he was homosexual or bisexual, based on his personal writings, artistic sensibility, and relationships. Because of Soviet laws against homosexuality, it is unlikely Eisenstein was ever public about his personal sexual preferences.

Eisenstein maintained very close working relationships with his crew, his students and various assistants. It can be argued he considered those personal relationships in a way he couldn't with a romantic partner. The exact nature of those personal relationships is unknown.