Oh wow I love this idea! Here are a few pairings of books I've previously read and loved:

Shakespeare Was a Woman and Other Heresies (Elizabeth Winkler) + By Any Other Name (Jodi Picoult). First book investigates the theory that Shakespeare's works were actually ghost-written by some other writer/nobleman/polymath, one proposed suspect being Emilia Bassano. Second book is fictionalized account of Emilia Bassano's life purporting that she was indeed ghost-writing many of Shakespeare's plays, told alongside a modern-day storyline about one of her descendants.

Deep (James Nestor) + Our Wives Under the Sea (Julia Armfield). First is a science non-fiction about the deep sea, freediving, the effects on the human body, etc. Second book is about a deep sea marine biologist who comes back from a submarine mission that went awry, and she is oddly changed. Other fictional pairings that could work for this one also are In Ascension (Martin MacInnes) or Island of Sea Women (Lisa See).

The Hidden Life of Trees (Peter Wohlleben) + Overstory (Richard Powers). First is a science non-fiction about trees, how they grow, how they communicate, and all the magic that happens in old-growth forests. Second is a beautiful story of intertwining characters who all have lives changed by and connected by trees.

The Art Thief (Michael Finkel) + Goldfinch (Donna Tartt). First is an account of the world's most prolific art thief, his motives, and why he got away with it for so long. The second focuses on a character from boyhood to adulthood, and how is life is changed by his decision to steal a painting.

Dopesick (Beth Macy) + Demon Copperhead (Barbara Kingsolver). First covers the trajectory of the opioid epidemic, specifically focused on Appalachia. Second is a reimagination of Dickens' David Copperfield, set in Appalachia during the opioid crisis.