PyCharm running Python file always opens a new console

Hi: If you are looking for re running the code again in the same python console everytime then you have to check the respective box in the Project settings as shown in image below.

To allow only one instance to run, go to "Run" in the top bar, then "Edit Configurations...". Finally, check "Single instance only" at the right side. This will run only one instance and restart every time you run.

There is a specific option in PyCharm 2018.2+: Settings | Build, Execution, Deployment | Console | Use existing console for "Run with Python console".

Run with Python console is an option you have enabled in the Run Configuration. Disable it if you don't need a Python console after a script execution: