Little is publicly known about Conway's early relationships before her transition. Societal norms and personal privacy likely played a role in keeping details private.

Lynn married Charles 'Charlie' Rogers in 2002. Their relationship was a source of great happiness and stability for Conway. Charlie was a supportive partner, actively participating in her advocacy work and providing companionship.

Conway cultivated many important friendships and mentorship relationships throughout her life. She had a close relationship with Carver Mead, her collaborator on the 'Introduction to VLSI Systems' textbook. She also mentored numerous transgender individuals in STEM fields, providing them with guidance and support.