It was a devastating performance from the Malaysian who has been at the top of his game all week and on this form looks set to land the first World title of his career in Sunday's final.
“I've prepared well for the tournament and I had to be at my best today,” Lee told reporters.
Smashing and recovering well, he had too much firepower for sixth-seeded Chen in the first game and then trailed 4-0 in the second.
However, Chen could not cash in. Chong Wei levelled at 7-7 and then sped away to book his place in a World Championship final for the first time.
“I thought I was average today and he was very good,” said Chen. “He was covering the court well.”
Chong Wei next plays three-times former champion Lin Dan of China or Europe's top player, Peter Gade of Denmark.
In the first women's semifinal, second seed Wang Yihan beat Chinese compatriot Wang Xin, last year's runner-up, 21-14, 21-15.
She next meets Germany's Juliane Schenk or Cheng Shao Chieh of Taiwan.
Earlier, top seeded Chinese pair of Wang Xiaoli and Yu Yang outclassed Japan’s third-seeded duo Maeda Miyuki and Suetsuna 21-8, 21-15 to enter the women’s doubles final.
Earlier on Friday, women’s top seed Wang Shixian tumbled out after suffering a straight-games loss. Her defeat came at the hands of colourful Taiwanese Cheng Shao Chieh, something of a walking fashion statement.
There was joy for an excited crowd at the Wembley Arena when the unseeded sole British survivors Chris Adcock and Imogen Bankier reached the last four of the mixed doubles.
China's Wang, the All England champion, lost 21-16, 21-17 to an effervescent Cheng, the ex-world junior champion who turned in a high-class display to dispose of the tournament favourite.
A tiring Wang was yellow-carded at 7-7 in the second game for taking too long towelling and from 11-11 the energetic Cheng moved up the gears. A series of fine winners were accompanied each time by a scream and trademark punch of the air with her left arm.
Noted for her cropped, dyed blonde hair, the tiny 25-year-old also sports an arm tattoo bearing her name, a necklace and white broad watch.
Cheng, world bronze medallist back in 2005, told reporters: “Maybe, I'm stronger and more mature now.”
Disappointed Wang said: “I need to go back and study her previous games more and maybe come back with a bit better idea of my tactics against her.”
German's Juliane Schenk handed Denmark's Tine Baun a heavy 21-9, 21-11 defeat in the other quarterfinal.
Home interest was kept burning when England's Adcock and Scotland's Bankier beat the Chinese fourth-seeds Tao Jiaming and Qing Tian 21-16, 21-18. Adcock said: “The feeling that went through me at the end was like nothing I had experienced before. It makes everything worth it. I hope we can put badminton back on the radar. Everything can be done and nothing is impossible.”