Poly(ethylene terephthalate) (PET)/Clay hybrids were prepared via in situ polymerization, in which the clay was modified with 12-aminododecanoic acid (ADA). Three types of bifunctional compounds were introduced into the system, respectively, as compatibilizers between PET and ADA-Clay. The three compounds contain 1 degree, 2 degree, and 3 degree amino groups, respectively, that could form ionic complex with carboxylic acid of ADA. They also contain an ester group that could react with PET chains through transesterification. The results show that adding the compound with 3 degree amino group can improve clay dispersion significantly, while the ones with 1 degree and 2 degree amino groups are not effective compatibilizers. The possible underlying mechanism is discussed.