Yacon roots contain about 80 wt% of -(2-1)-fructooligosaccharides (FOS). This work aims to use water extraction method combined with sugaring-out technology to extract FOS from yacon. Most of FOS was extracted into the acetonitrile (ACN)-rich top phase, when yacon roots were dissolved in an ACN-yacon water extract mixture without extra sugar addition. Experimental results indicated that the partitioning behavior of FOS was closely correlated with the concentration of sugar in water extract of yacon, the system temperature and the volume ratio between ACN solution and yacon water extract.