The effect of graphene oxide (GO) on the morphology and properties of monomer casting polyamide 6/polystyrene (PA6/PS) alloy was evaluated. PA6/PS/GO ternary alloys were prepared by the double in situ polymerization of ε-caprolactam and styrene monomer. SEM results show that phase inversion occurred in this system when the GO content was 0.5 wt%. A morphology of PA6 microsphere dispersed phase/PS matrix was formed. TEM results show that the GO lamellae were selectively and homogeneously dispersed in PA6 microspheres. When the GO content reached 1 wt% or 1.5 wt%, the system did not reverse completely, forming a structure of PA6 block or PA6 network continuous phase and local PA6 microsphere dispersed phase/PS continuous phase. GO lamellae were dispersed in PA6 blocks or PA6 network continuous phases. With the increase in the molecular weight of PS in PA6/PS/GO alloy, when the GO content reached 1.5 wt%, the system still maintained the morphology of PA6 microspheres. A larger molecular weight of PS is good for phase inversion, while GO inhibits the phase inversion of PA6/PS alloy. GO lamellae always distributed to the PA6 phase no matter which phase it was predispersed. XRD and DSC spectra show that GO can slightly affected the crystallization of PA6, decreased the crystallization rate of PA6. The antibacterial test results show that the alloy containing 1 wt% GO has an antibacterial rate of up to 95% against Escherichia coli. This selective dispersion phenomenon is of great significance for the study and application of the compatibility of polymer alloy phases.