Shen Longyuan started his professional football career in 2004 after he graduated from the Shanghai Shenhua youth team. He would make his league debut for Shenhua against Qingdao Zhongneng on October 23, 2004, coming on as a late substitute in a 1–0 defeat.[1] After that defeat he would only play in one more league game throughout the season, however he would continue to establish himself the following seasons as a reliable squad regular within the team. By the 2006 league season he would gain more playing time and on September 9, 2006, Shen would go on to score his first league goal against Beijing Guoan in a 1–0 victory.[2] With the introduction of Jia Xiuquan as manager during the 2008 league season Shen would actually start to become a permanent member of the first team, however this was out of position at full back during the absence of Sun Xiang. When Miroslav Blažević came in as manager at the beginning of the 2010 league season he stopped playing Shen out of position but ignored him throughout most of the season and rarely played him at all.
After his contract expired at the end of the 2010 league season he would leave Shanghai Shenhua and subsequently join Hangzhou Greentown in January 2011 where he was reunited with one of his former Shenhua managers Wu Jingui. On March 1, 2011, in Hangzhou's first game of the season Shen would make his debut against Nagoya Grampus in a 2011 AFC Champions League group stage game, Which Hangzhou won 2–0.[3]