I have installed python3.9 from MS Store and in command line it’s available via python command. but jupyter cannot find python.
Hi Mohammad, welcome 
It looks like you are using a Jupyter extension for your editor which being developed by Microsoft rather than by the Project Jupyter community.
This is obviously fine and it’s fine to keep this post here and you might indeed receive a useful response, but just in case if there is nobody to help you (just because members of the community here might be using different editors, like Jupyter Notebook or JupyterLab), I will point you to the place where the extension authors recommend to ask questions, which is Stack Overflow with tags as in link; if this seems like a bug you can also fill an issue on their issue tracker.
Sorry I cannot help myself (I don’t think Microsoft Store is available on Linux). I hope you will find a solution and enjoy the extension you are trying to configure.
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Thank you! I’ll fill a new issue on github.