We have fabricated well-ordered organic donor/acceptor nanojunction arrays comprising p-sexiphenyl (6P) and C60 via self-assembly of C60 on the molecular nanotemplate of 6P nanostripes on Ag(111). Our scanning tunneling microscopy measurements show that the preferential trapping of C60 triplets atop 6P single molecule leads to the formation of the C60/6P vertical nanojunctions with well-defined two-dimensional arrangement. Annealing this binary molecular superstructure at 380 K results in the insertion of C60 linear chains between the neighboring 6P nanostripes and thereby the appearance of the periodic C60/6P lateral nanojunction arrays.