The sale is expected to close in the first quarter of 2016, pending regulatory approval. Financial terms have not been disclosed.
Chi-X Global chief executive Tal Cohen said JC Flowers has a "deep appreciation" for the Australian, Japanese and Hong Kong markets.
"[JC Flowers] shares our vision of leveraging technology to develop innovative market-level solutions that enhance investor performance," Mr Cohen said.
"We believe that Chi-X will continue to deliver greater choice and cost-effective solutions to investors and issuers as JC Flowers & Co builds on the Chi-X brand," he said.
JC Flowers managing director Thierry Porte said the three Chi-X businesses have established themselves as "successful and innovative alternatives" to the primary exchanges in Australia, Japan and Hong Kong.
"Their superior technology, service and trade execution performance will continue to drive positive change and improve markets where they operate," Mr Porte said.
"We hope to accelerate this growth through continued enhancements to the platform, including new investment products and markets, and by leveraging our strong relationships throughout the Asia Pacific region," he said.
JC Flowers & Co has more than US$10 billion of capital in 24 portfolio companies in 15 companies.
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