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In 1994, Li joined IDD Information Services; a New Jersey division of Dow Jones and Company, where he helped develop a software program for the online edition of The Wall Street Journal. He also worked on improving algorithms for search engines. He remained at IDD Information Services from May 1994 to June 1997.

In 1996, while at IDD, Li developed the Rankdex site-scoring algorithm for search engine page ranking, which was awarded a U.S. patent. He later used this technology for the Baidu search engine.Li has worked as a staff engineer for Infoseek, a pioneer internet search engine company, from July 1997 to December 1999.

Another of his important innovative achievements was the picture search function used by Go.com.

In the twelve years since founding Baidu in January 2000, Li has turned the company into the largest Chinese search engine, with over 80% market share by search query, and the second largest independent search engine in the world. On August 5, 2005, Baidu successfully completed its IPO on NASDAQ, and in 2007 became the first Chinese company to be included in the NASDAQ-100 Index.

He appeared in CNN Money's annual list of "50 people who matter now" in 2007.