Although the structure of Cu(100)-()R45°-O missing row reconstruction (MRR) has been well-established for decades, the detailed structure of its various boundaries remains an untilled area due to the difficulties in obtaining atomically resolved images. Herein, atomic arrangement of the phase boundaries existing in MRR structure was modeled on the basis of scanning tunneling microscopy (STM) investigations. By determining the periodicity and unit structure of MRR in STM images and extending them to boundary region, several types of phase boundaries were identified, resulted respectively from: (1) the mismatch between c(2 × 2)-O patches, (2) the regulation by step edges, and (3) the mismatch between Cu missing rows (MRs). With the modeled structure, it was revealed that the types of the c(2 × 2)-O mismatch induced phase boundaries (OMIPBs) are mainly dominated by the oxygen exposure and in-diffusion barrier. The step edge regulated phase boundaries (SERPBs) are always terminated with Cu-O chain and may represent an intermediate growth stage to larger MRR structure. Comparatively, Cu MRs mismatch is often reconciled by the differently oriented domains between them. As a result, the Cu MRs mismatch induced phase boundaries (CMRMIPBs) are only occasionally observed as Cu-O chains between mismatched Cu MRs that encounter shoulder-to-shoulder. For all studied boundaries, the surrounding MRR domains exhibit obvious orientation preference through inclined packing along the SP direction with the degree closely related with the width of the boundaries.