Study Background: Hybanthus enneaspermus medicinal plant are the natural reservoir of medicinal compounds to cure many diseases since the compounds have no adverse side effects. The current study focused on characterization of chemical compounds present and their in-silico anti-viral activity by adopting molecular drug designing method. Objective: SARS-CoV-2 outbreaks resulted approximately around one lakh deaths in all over the world. Still there is no particular drug for the viral infection treatment. To overcome and control this fatal infection, medicinal plants are the versatile solution with less side effects when compared to synthetic drugs. The Covid-19 spike protein, the key protein in viral transmission of host cells by membrane fusion mechanism. The main research of this work is to investigate the Hybanthus enneaspermus phyto-compounds by In-silico molecular drug designing approach against Covid-19 spike protein. Methodology: Molecular docking analysis of Hybanthus enneaspermus phytocompounds resulted from FT-IR and GC-MS analytical studies. The molecular drug designing softwares such as ACD Chemsketch, AutoDock 4.2 version and 3D molecular visualization UCSF Chimera software were used. Results: Our study reports the phytochemical analysis of crude extract of Hybanthus enneaspermus. FT-IR, GC-MS revealed compounds were docked against SARS-CoV-2 proteins and lead compounds were summarized using MGL tool AutoDock vina 4.2 version. Docking results suggested that 3-Trifluoroacetoxypentadecane (-8.9), 9,12-Octadecadien-1-ol (-8.6), 9,12,15-Octadecatrienoic acid (-8.8), 9,12-Octadecadienoic acid (- 9.2 ) had high binding affinity with minimum binding energies scoring function and hence considered as potential anti-viral inhibitory activity. Conclusion: Our molecular drug designing approach using Hybanthus enneaspermus data demonstrated that ability of designing of anti-viral drug against SARS-CoV-2. Moreover, this study suggested to perform in-vitro and in-vivo experiments to understand therapeutic effect much more better.