The societies with high fertility rate exposed very less rate of son preference over daughter. But the fertility decline has a linkage of greater demand for son than daughter. In Manipur, a high proportion i.e. 31.2% of married women want more sons than daughters according to NFHS-3 which is declining from that of 36.5% in NFHS-2 and 43.4% in NFHS-1, so that, the factors associated with desire of more sons have caused high fertility indices in the state. The objective of this study is to investigate the socio-demographic determinants of fertility differential and the third birth transition. This is a cross sectional, community based study of 1296 women and was conducted through a cluster sampling scheme in four valley districts of Manipur-Bishnupur, Imphal East, Imphal West and Thoubal. The multiple and logistic regression models are adopted in addition to the classical statistical tests. Results show that, the age at marriage, education, income, desire number of son, duration of marriage, infant mortality etc. have significant contribution on the variation of fertility indices. One of the most important determinants of the fertility indices is son preference which is quantified by desire number of son in one way or others. The son preference is most important factor among other socio-demographic determinants of fertility differentials in Manipur. The findings may be useful in community maternal health management.