Population synthesis is the foundation of the agent-based social simulation. Current approaches mostly consider basic population and households, rather than other social organizations. This article starts with a theoretical analysis of the iterative proportional updating (IPU) algorithm, a representative method in this field, and then gives an extension to consider more social organization types. The IPU method, for the first time, proves to be unable to converge to an optimal population distribution that simultaneously satisfies the constraints from individual and household levels. It is further improved to a bilevel optimization, which can solve such a problem and include more than one type of social organization. Numerical simulations, as well as population synthesis using actual Chinese nationwide census data, support our theoretical conclusions and indicate that our proposed bilevel optimization can both synthesize more social organization types and get more accurate results.