We demonstrate that the molecular ligands play important roles in controlling the electronic states and electron transport properties of single cobalt (Ⅱ) octaethylporphyrin (CoOEP) molecule adsorbed on Au(111) surface by using low-temperature scanning tunneling microscopy and spectroscopy. Single CoOEP molecule adsorbed on Au(111) surface has eight methyl groups pointing out of the surface plane. A peak located at -50 mV in dI/dV spectrum measured on the Co atom of CoOEP is identified as a d-orbital mediated resonance. We find that the methyl groups in CoOEP can be removed in a stepwise manner, and finally lead to a fully-demethylized CoOEP. The d-orbital mediated resonance gradually evolves into a sharp Kondo resonance located right at Fermi level in the demethylization process. Both experimental and theoretical results indicate that the chemical environment and magnetic moment of the central Co atom change slightly in the fully-demethylized CoOEP: the Co atom is slightly lifted by 0.15 and the magnetic moment increases from 0.5 B to 0.6 B. The emergence of Kondo effect is qualitatively explained with a simple model by consideringthe change in the tunneling parameters of the ligands upon demethylization. We also show that the transport properties of the CoOEP can be dramatically controlled by weak intramolecular van der Waals interaction. In CoOEP closely-packed dimers and trimers where CoOEP molecules are introduced close enough to each other, the ethyl groups in the neighboring area are found to be strongly lifted by 0.4 . More surprisingly, a pronounced resonance shows up at 00.8 V in the dI/dV spectra of the lifted ethyl groups. High resolution spectra show that the new resonance consists of multiple peaks with equal spacing of 137 8 mV. The spacing energy coincides with the vibrational energy of stretching mode of CC bond between ethyl group and the brim carbon atom of the porphyrin ring. Therefore the newly-emerged resonance is attributed to the vibronic states originating from the intramolecular CC bond stretching mode excited by tunneling electrons. A model considering the local formation of a barrier between the lifted part of the molecule and the substrate is employed to explain the experimental observations. Our findings show that the electron transport properties in single molecules can be intensely tuned by controlling the chemical properties of the molecular ligands.