To investigate the impact of matter mixing on the formation of molecules in the ejecta of SN 1987A, time-dependent rate equations for chemical reactions are solved for one-zone and one-dimensional (1D) ejecta models of SN 1987A. The latter models are based on the 1D profiles obtained by angle-averaging of the three-dimensional (3D) hydrodynamical models, which effectively reflect the 3D matter mixing; the impact is demonstrated, for the first time, based on 3D hydrodynamical models. The distributions of initial seed atoms and radioactive 56Ni influenced by the mixing could affect the formation of molecules. By comparing the calculations for spherical cases and for several specified directions in the bipolar-like explosions in the 3D hydrodynamical models, the impact is discussed. The decay of 56Ni, practically 56Co at later phases, could heat the gas and delay the molecule formation. Additionally, Compton electrons produced by the decay could ionize atoms and molecules and could destroy molecules. Several chemical reactions involved with ions such as H+ and He+ could also destroy molecules. The mixing of 56Ni plays a nonnegligible role in both the formation and destruction of molecules through the processes above. The destructive processes of carbon monoxide and silicon monoxide due to the decay of 56Ni generally reduce the amounts. However, if the molecule formation is sufficiently delayed under a certain condition, the decay of 56Ni could locally increase the amounts through a sequence of reactions.