Lim Kim San died from pneumonia and old age on 20 July 2006. He was 89, just four months short of turning 90. He had been ill from a lung ailment and had to spend long stints in hospital, but he passed away peacefully at his Dalvey Road home, surrounded by his family, his beloved koi fish, and his memories of his wife, who had died in 1994.

His children remember him as a man of integrity and impartiality who never made much of his position as a minister but who taught them, instead, the need for empathy with people from all walks of life. Believing that charity begins at home, he shared the fruits of his business success through the entire extended family. He was a conservative patriarch, but he tried to be emphatically fair as well.

Lim was a private man who kept his six children out of his political life. Daughter Lim Siew Tin said: “We kept a low profile. Father did not like our telling people who we were because he was worried that they would ask him for favours.” Indeed, Lim Kiat Seng, his eldest son, recalled that he would turn away relatives who wanted to meet him to seek favours. But that did not mean that politics did not pursue the family. “Father was known as a cleaner,” Lim Siew Tin said. “He cleaned up ministries. He stepped on a lot of toes, but did not care about what people thought about him.” That cost the family dear at times. She recounted how a nephew of hers had been punished in a leading school for being Lim's grandson. “He was made to stand on the table while the teacher taunted him, saying that a minister's grandson was so ill-behaved that he had to be punished.” In her account, the teacher was against certain policies of the Ministry of National Development, which Lim headed, and took out her anger on the child. “A teacher in the same school picked on my daughter so much that I had to withdraw her from it. But my father did not interfere,” Lim Siew Tin said.