Since 2008, Thurston has been in a relationship with Samantha Lynch. In June 2013, the couple had their first child together; a daughter they named Frankie Louise Thurston. In March 2015 the pair welcomed their second daughter Charlie Grace Thurston. On 3 November 2015, Johnathan and Samantha 'eloped' to Hamilton Island to marry in a private ceremony with their daughters and parents present. This news was broken by Sam on her Instagram. The couple welcomed a third daughter, Lillie Rose Thurston, on 22 March 2017. Their fourth daughter, Remie Lee, arrived in February 2019.