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Controlling the atomic configurations of structural defects in graphene nanostructures is crucial for achieving desired functionalities. Here, we report the controlled fabrication of high-quality single-crystal and bicrystal graphene nanoislands (GNI) through a unique top-down etching and post-annealing procedure on a graphite surface. Low-temperature scanning tunneling microscopy (STM) combined with density functional theory calculations reveal that most of grain boundaries (GBs) formed on the bicrystal GNIs are 5-7-5-7 GBs. Two nanodomains separated by a 5-7-5-7 GB are AB stacking and twisted stacking with respect to the underlying graphite substrate and exhibit distinct electronic properties, forming a graphene homojunction. In addition, we construct homojunctions with alternative AB/twisted stacking nanodomains separated by parallel 5-7-5-7 GBs. Remarkably, the stacking orders of homojunctions are manipulated from AB/twist into twist/twist type through a STM tip. The controllable fabrication and manipulation of graphene homojunctions with 5-7-5-7 GBs and distinct stacking orders open an avenue for the construction of GBs-based devices in valleytronics and twistronics.