Lin, a four-time world champion, dominated the match, taking 46 minutes to beat his great rival 21-16, 21-14, and ending the Malaysian's record of reaching the final of every Open tournament he has played this year.
Lee had been many people's favourite to win at the Hong Kong Coliseum following an indifferent recent run by Lin, who has again courted controversy by forfeiting matches against Chinese team-mates through injury or illness.
But Lee could not avenge his heart-breaking world final loss to Lin and in a match between the two dominant players of their generation, it was the Chinese shuttler who was once again on top.
In August Lee let slip two match points as Lin, the sport's most decorated player, crawled off the canvas to claim his fourth world title in London. Lin also beat Lee in the finals of the 2008 Olympic and 2010 Asian Games.
He now faces a final against either second seed Chen Long or Chen Jin, who play later in an all-Chinese semifinal.
In the women's draw Denmark's Tine Baun overcame China's new world number one Wang Shixian 21-10, 19-21, 21-13, with the European champion smashing her way to victory.
She will face either Wang Yihan or Wang Xin in the final.
In the women's doubles the two dominant pairings of the season will face off in an all-Chinese final after Tian Qing/Zhao Yunlei beat Denmark's Christinna Pedersen/Kamilla Rytter Juhl 21-18, 21-13, and Wang Xiaoli/Yu Yang won against South Korea's Jung Kyung-Eun/Kim Ha-Na 21-18, 21-12.
Lin beats Lee in Hong Kong semifinal
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