In this research, a heterogeneous Nano-Structured functionalized SBA-15 metformin palladium composite catalyst is reported for the selective hydrogenation of alkynes. In the first place, A series of the heterogeneous mesoporous SBA-15 metformin palladium catalyst were prepared and afterwards the condition and the ratio of used materials were optimized to give rise a suitable high performance catalyst. The final nano-structured catalyst was characterized by X-ray powder diffraction, BET surface area, FT-IR spectrophotometer, Scanning electron microscopy (SEM) and Transmission electron microscopy (TEM) and served in partial hydrogenation of different alkynes, with high selectivity and high yield. The liquid phase hydrogenation was conducted under mild condition of room temperature and atmospheric pressure. The reactions were monitored every half an hour by gas chromatography and all of them were completed during 4-6 hours. The products were characterized by 1H-NMR, 13C-NMR, FT-IR, and Mass Spectrometry (MS) that strongly confirmed the (Z)-double bond configuration of produced alkenes. This prepared catalyst is competitive with the best palladium catalysts known for the selective liquid phase hydrogenation of alkynes and can be easily recovered and regenerated with keeping high activity and selectivity over multiple cycles with a simple regeneration procedure.