Quantum well intermixing (QWI) by the impurity-free vacancy disordering (IFVD) technique is an important and effective approach for the monolithic integration of optoelectronic devices based on InGaAs/InP quantum well structures. We experimentally investigate the influence of the capping layer SiO2 and Si3N4 on the QWI by IFVD. The results show that for all the samples with three-types differently doped (P, N and I) top InP layers, Si3N4 can always induce a larger photoluminescence blueshift than SiO2 in the IFVD QWI process, which attributes more to the group III and V vacancies point defects created in the interface of Si3N4-InP than that of SiO2-InP, proved by the SIMS measurements. The inherent mechanisms for explaining these properties are further discussed.