Layered three-dimensional (3D) topological semimetals have attracted intensively attention due to the exotic phenomena and abundantly tunable properties. Here we report the experimental evidence for the 3D topological semimetal phase in layered material TaNiTe5 single crystals through quantum oscillations. Strong quantum oscillations have been observed with diamagnetism background in TaNiTe5. By analyzing the de Haas-van Alphen oscillations, multi-periodic oscillations were extracted, in content with magnetotransport measurements. Moreover, nontrivial {pi} Berry phase with 3D Fermi surface is identified, indicating the topologically nontrivial feature in TaNiTe5. Additionally, we demonstrated the thin-layer of TaNiTe5 crystals is highly feasible by the mechanical exfoliation, which offers a platform to explore exotic properties in low dimensional topological semimetal and paves the way for potential applications in nanodevices.