Fabrication of device though bottom-up approach and using nanowires as building blocks has received significant attention as one can build flexible electronics which can handle stress better than thin film based device. However successful joining of the nanowires for fabrication of such device remains a challenge till date. While several well researched joining techniques are available for metal based nanowires, the same for ceramic nanowires is scarce at present. In this work we explore ion beam induced formation of heterojunction between two metal oxide nanowires, namely hydrogen titanate (H2Ti3O7) and cuprous oxide (Cu2O). The electron microscopy studies reveal detailed structural modifications at the joining sections. The ion beam modifications are explained using state-of-the-art TRI3DYN simulations, which details about migration of atoms, defects, sputtering, redeposition and atomic mixing between the two nanowires and emphasize that such junction formation is caused mainly due to atomic collisional effects.