On April 10, 2008, he created controversy when he struck coach Ji Xinpeng in front of his teammates and reporters during the warm-up tournament ahead of the Thomas Cup. The incident was reportedly triggered by Lin being unhappy with Ji's starting lineup for the tournament.
Lin has been in a romantic relationship with Xie Xingfang, herself a former world champion badminton player, since 2003. They were quietly married on December 13, 2010 in Haizhu, Guangzhou. Xie initially denied but later admitted the news when reporters got the evidence. Lin reacted angrily towards the news and insisted that it was a personal matter between him and Xie.
However, Lin's hope to become the first player to win five All England titles in the open era was dashed when he was defeated by Lee Chong Wei in the final. He then won his second Asian Championships in April on a day which saw China sweep all five titles. Lin helped China to a fourth consecutive Sudirman Cup title in May, defeating Denmark 3–0 in the final. In June, Lin withdrew from the Singapore Open final due to gastric flu, this drew the jeers from fans in the stadium. Just few days later, he was stunned by Sho Sasaki in the second round of Indonesia Open.
In August, he won his fourth World Championships title by beating Lee Chong Wei in final in Wembley Arena, a venue which will host the same competition for 2012 Summer Olympics. This dashed Lee's hope of becoming the first Malaysian to win gold medal in World Championships.
In September, he was ousted in the semi-finals of China Masters, and withdrew from the semifinals of Japan Open. This was followed up by a shock exit in the second round of the Denmark Open to Hong Kong player Wong Wing Ki, and retired in the semifinals of French Open despite leading the match, stated it is due to paronychia. The retirement also marked his sixth in the season, many media quest the retirement was due to the strategic consideration to let China team have full quota in men's singles for 2012 Olympics. However, Li Yongbo said Lin retirement is not a "gift", this is due to that BWF stated that each top players are compulsory to participate in number of tournament and Lin needs a better condition towards the Olympics. Lin voice frustrated that the peak schedule was the reason he had a most retirement in a season. In November, he won his fifth Hong Kong Open title.