Formation of nanowire networks is an appealing strategy for demonstration of novel phenomena at nanoscale, e.g. detection of Majorana fermions, as well as an essential step towards realization of complex nanowire-based architectures. However, a detailed description of mechanisms taking place during growth of such complex structures is lacking. Here, the experimental observations of gold-catalyzed germanium nanowire junction formation are explained utilizing phase field modelling corroborated with real-time in-situ scanning electron microscopy. When the two nanowires collide head-on during the growth, we observe two scenarios: (i) two catalytic droplets merge into one and the growth continues as a single nanowire, or (ii) the droplets merge and subsequently split again, giving rise to the growth of two daughter nanowires. Both the experiments and modelling indicate critical importance of the liquid-solid growth interface anisotropy and the growth kinetics in facilitating the structural transition during the nanowire merging process.