The 63-year-old actress said she felt “unlovable” after finding out about the fling which ended her and her husband’s six-year marriage in 1995.
Love Actually star Emma had married film director Kenneth, 61, in 1989 – just two years after they met.
Thompson said: “I was utterly, utterly blind to the fact that he had relationships with other women on set.
“What I learned was how easy it is to be blinded by your own desire to deceive yourself. I was half alive.
“Any sense of being a lovable or worthy person had gone completely.”
Branagh and Bonham-Carter, 56, played each other’s love interests in Mary Shelley’s Frankenstein, which he also directed, when it is believed they had an affair.
The pair went on to have a five-year relationship. Two years before they started the affair, Bonham-Carter co-starred with Thompson on acclaimed 1992 film Howards End.
The actresses have since worked together in films of the Harry Potter series, with Thompson playing Professor Trelawney and Bonham-Carter in the role of Bellatrix Lestrange.
Thompson has said she had “forgiven” Bonham-Carter. In 2013, she said it was “all blood under the bridge”, adding: “You can’t hold on to anything like that.
“It’s pointless. I haven’t got the energy for it. Helena and I made our peace years and years ago.”’
The star said it was her actor husband Greg Wise, who she has been married to for 27 years, who “picked up the pieces and put them back together”.
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She said: “’I’ve learned more from my second marriage just by being married. As my mother says, ‘The first twenty years are the hardest.’”
The pair met while filming Sense and Sensibility in 1995, which was scripted by Thompson. She later won the Oscar for Best Adapted Screenplay.
They married in 2003 and have two children, daughter Gaia, 22, and son Tindyebwa, a former child soldier from Rwanda who they informally adopted when he was 16.
Branagh married art director Lindsay Brunnock the same year and they are still together. They met on the 2002 Channel 4 mini-series Shackleton.
Meanwhile, Bonham Carter has two children, Billy and Nell, with her ex-partner – film director Tim Burton. The pair split after 13 years together.
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