A Family Matter jumps between the story of a father and daughter in the present day and 1982 to reveal why the mother had disappeared from their lives.
Lynch said she was inspired after discovering a statistic saying up to 90% of lesbian women who were married to and had children with men in the 1980s lost legal custody of their children in divorce cases.
She told BBC Radio 4’s Woman’s Hour there was “pressure put upon families to say, the best thing to do in this situation is to remove this source of embarrassment and shame, to take this mother away from the family”.
She said: “The intention was, in the best case scenario, the child would be very young, they would forget, and the family could sort of reform around the scar, if you like, and carry on as if that woman had never been there.”
The author researched real cases using court transcripts and newspaper articles.
“The stuff in the court cases – I couldn’t make it worse, to be honest, so I brought things from real court cases and put them together.”
A Family Matter is the first debut novel to win the overall prize at the Nero Book Awards or their predecessors, the Costa Book Awards, since 2013.
Lynch will receive a £30,000 prize, while the other category winners will each receive £5,000.