In his early years, Lee favoured basketball, however his mother soon forbade him from the game due to the searing heat of the outdoor basketball court. Lee began to learn badminton at the age of 11, when his father, who liked to play the game, brought him to the badminton hall. Attracting the attention of a local coach, the coach asked Lee's father if he could take him as a student. After receiving his father's consent, the coach began to train Lee after school.
Discovered by Misbun Sidek, he was drafted into the national squad when he was seventeen years old. On 3 November 2006, Lee was involved in a car accident. On his way to Bukit Jalil after dinner, he was hit from behind by a vehicle which had lost control after a tire blow out. He was then sent to the Sunway Medical Centre and treated with six stitches for his head injury. Lee received RM300,000 on 21 August 2008, as a reward for his silver medal effort in the 2008 Olympic Games. Also, he received RM3,000 a month as a lifetime pension beginning in August 2008.
For the same achievement, he was conferred with a Darjah Setia Pangkuan Negeri (DSPN), which carried the title Datuk by Governor of Penang, Tun Abdul Rahman Abbas on 30 August 2008. He was appointed as UNICEF Malaysia's National Ambassador in February 2009. On 6 June 2009, Lee received the Darjah Bakti (DB) award, from Tuanku Mizan Zainal Abidin, in conjunction with the Birthday of Seri Paduka Baginda Yang di-Pertuan Agong, for his achievements in the 2008 Olympics. He was in a relationship with Wong Mew Choo, his teammate.
In 2009, Lee and Wong announced they are no longer together during the 2009 World Championships in Hyderabad, India. However, Lee announced his reconciliation with Mew Choo after winning a silver medal in 2012 Summer Olympics. They were married on 9 November 2012, and had their first child, named Kingston in April 2013. On 16 March 2011, Lee received Permodalan Nasional Berhad shares worth MYR100,000 from Najib Tun razak soon after his triumph in the All England Open. He was appointed as KDU University College ambassador on 31 July 2011. Lee's autobiography Dare to be a Champion was officially published on 18 January 2012.