The Aldershot, Farnham & District athlete completed a hat-trick of wins around the streets of Southsea on Sunday.
Thompson powered home with a personal-best time of 46min 56sec, beating Stubbington-born Andy Vernon (47.29).
Eilish McColgan (54.43) won the ladies' race in style.
Thompson has forged a close affinity with the Portsmouth crowd after a third straight Great South Run success.
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The 37-year-old lauded those who congratulated him afterÂ his triumph '“Â comparing it to a footballer celebrating a goal with their fans.
Thompson said: '˜The really amazing thing for me wasÂ when I wasÂ warming up there was a very knowledgeable crowd saying 'good luck, I hope you get the three-timer'.
'˜Afterwards, the number of people who came up to me saying they were really happy for me was overwhelming.
'˜For me, it is a lonely sport. You put a lot of miles in on your own and you're mentality toughing it out.
'˜But to share the victories with family, friends and so my supporters is a real joint-moment.
'˜It's the closest in my sport to scoring a goal in football. Everyone cheers with you in football and I felt like I had that.
'˜It wasÂ an overwhelming feeling, an amazing day and I'll never forget it.'