Emperor Ruizong made Song the minister of civil service affairs () and gave him the designation "Tong Zhongshu Menxia Sanpin" (), making him a chancellor "de facto". After Li Longji was created crown prince, Song was also made a member of his staff. During Emperor Zhongzong's reign, the civil service affairs system was subject to great abuses by powerful individuals at court, particularly while the chancellors Cui Shi and Zheng Yin were in charge — as they were allowing bribes and pleas by powerful individuals to influence them, going as far as naming reserve officials two years in advance. Song and his deputies Li Ai () and Lu Chongyuan () reformed the system and put the civil service system back in order, at the same time that Song's fellow chancellor Yao Yuanzhi, who was then also minister of defense, put the military promotion system back in order as well. It was said that popular sentiment at the time viewed this as the return to the clean government of the days of Emperor Gaozong's father Emperor Taizong. Song's reforms included removing all of the several thousands of officials that Emperor Zhongzong commissioned directly without submitting the commissions to the examination bureau for review.