Metal-phthalocyanines (MPcs) and their derivates have attracted increasing interest in recent years, due to their potential applications in molecular electronics, spintronics, sensors, and so on. To this end, it is essential to tune the structural, electronic and spin properties of MPcs. Using the low-temperature scanning tunneling microscopy (LT-STM), we demonstrate that the spin, chirality and adsorption site of MnPc on Au(111) surface can be tuned by hydrogen atoms. STM experiments and density functional theory (DFT) calculations reveal that the preferential adsorption sites for the MnPc molecules may switch from the fcc regions to the hcp regions on the Au(111) surface after a hydrogen atom is adsorbed on top of the central Mn ion of each MnPc molecule. Moreover, the molecular spin decreases from S=3/2 to S=1 and the molecule-substrate coupling is weakened after the adsorption of a hydrogen atom on a MnPc molecule, leading to the quenching of Kondo effect at 4.2 K. However, the molecular spin and Kondo effect can be recovered by local voltage pulse or sample heating. Adsorption of three hydrogen atoms on a MnPc molecule not merely lowers the molecular symmetry from 4-to 2-fold, but also breaks down the mirror symmetry of the entire adsorbate complex (molecule and surface), thus rendering it to become chiral without any realignment at the surface. Dehydrogenation of the adsorbate by means of inelastic electron tunneling can also restore the mirror symmetry of the adsorbate complex. STM experiments as well as DFT calculations show that the chirality is actually imprinted into the molecular electronic system by the surface, i.e., the lowest unoccupied orbital is devoid of mirror symmetry. Our novel reversible spin and hand control scheme can be easily realized at single-molecule level, thus opening up a new avenue to broader applications based on the molecular electronic and spin states.