Charles Thomas was the eldest son and second children of Dominic Marquard, 2nd Prince of Löwenstein-Wertheim-Rochefort (1690–1735) and his wife Christine Franziska Polyxena (1688–1728) a daughter of Charles, Landgrave of Hesse-Wanfried by his second wife Countess Juliane Alexandrine of Leiningen-Dagsburg.

On 7 July 1736 in Vienna he married Princess Maria Charlotte of Holstein-Wiesenburg (1718–1765), daughter of Leopold, Duke of Schleswig-Holstein-Sonderburg-Wiesenburg.

Their only child and daughter Leopoldine (1739 – 1765) married in 1761 her cousin, Charles Albert II, Prince of Hohenlohe-Waldenburg-Schillingsfürst (1742–1796).

After the death of his first wife, he married morganatically on 4 February 1770 Maria Josepha von Stipplin (1735–1799).

After more than fifty years as reigning prince and without legitimate male heirs, Charles Thomas was succeeded after his death by his nephew, Dominic Constantine (1762–1814), son of his youngest brother Prince Theodor Alexander of Löwenstein-Wertheim-Rochefort (1722–1780).