We present the magnetoresistance (MR) and Hall resistivity of layered ternary Nb3SiTe6 thin flakes with magnetic field up to 33 T. The flakes show strong angle-dependent MR properties and unsaturated quasilinear dependence accompanied with Shubnikov-de Haas (SdH) oscillations. Hall resistivity study demonstrates that the hole carriers dominate the transport properties in the whole temperature range. The angle-dependent SdH oscillations reveal a two-dimensional Fermi surface of Nb3SiTe6. Furthermore, by analysis of SdH oscillations, we observed a nontrivial \Berry phase in the SdH oscillations which suggests the nontrivial topological nature of Nb3SiTe6. \ 2018 American Physical Society.