Lee, 21, was named Player of the Year, Players' Player of the Year and best newcomer.
The South Korea winger arrived in the summer from FC Seoul after being recruited by former manager Gary Megson, who departed the club in January and was replaced by Owen Coyle.
Lee came on in the second half on Sunday as Bolton finished their campaign by beating Birmingham 2-1.
Kevin Davies made the breakthrough and won the Golden Boot after finishing top scorer with nine goals.
On-loan striker Ivan Klasnic took the seasonal man of the match award while Gretar Steinsson was named the Community Player of the Year.
Source: Team Talk
Source: Team Talk