Coherent phonon scattering and transmission via a three-terminal junction in low-dimensional structures is investigated. The model system consists of two-dimensional crystalline wave-guides, constructed of double atomic chains that are joined together by a nanostructured T-shaped junction. The matching method theoretical approach is used to study the dynamics of the system. A calculation is presented for the coherent reflection and transmission scattering probabilities of the system phonons, as elements of a Landauer type scattering matrix. The scattering and transmission spectra via the T-shaped junction are analyzed as a function of the incident frequency per propagating mode of the perfect wave-guides. Our results show that the junction is an effective phonon splitter and suggest that its characteristics may be controlled by varying its nanometric parameters. Asymmetric Fano-like resonances are observed in the spectra which result from the coherent coupling between the localized modes of the T-shaped junction and the propagating modes of the wave-guides.