Chua was born in Singapore in 1905 to Chua Kim Teng, a wealthy local businessman, and Liong A Soen (aka Neo Ah Soon), a Chinese Indonesian of Hakka descent who hailed from Pontianak, West Kalimantan, Dutch East Indies (present-day Indonesia).

While her father was born in Singapore, her paternal grandfather came from a Hokkien Peranakan family in Malacca, Malaysia with ancestry from Haicheng, Zhangzhou, Fujian.

[1][2] Her parents then arranged a marriage for her to a storekeeper named Lee Chin Koon and they married when she was sixteen, whilst he was eighteen years old in 1921.

[3][4] Chua saved her family jewelry and money, managing household finances and helping Kuan Yew attend law school in Britain.

Chua, a nyonya (Peranakan Chinese woman), was considered a "highly respected authority" on the subject.