If you are looking to pass a environment variable that is defined by in run config, then it is not possible.
If you want to edit the configuration in file. Then usually it is stored in .idea/workspace.xml. This has all the run configurations and everything stored.
I don't have clion but have PyCharm, any a sample from same is
...
...
<configuration name="scrape2" type="PythonConfigurationType" factoryName="Python" temporary="true">
<module name="scripts" />
<option name="INTERPRETER_OPTIONS" value="" />
<option name="PARENT_ENVS" value="true" />
<envs>
<env name="PYTHONUNBUFFERED" value="1" />
</envs>
<option name="SDK_HOME" value="" />
<option name="WORKING_DIRECTORY" value="$PROJECT_DIR$/deprecated" />
<option name="IS_MODULE_SDK" value="true" />
<option name="ADD_CONTENT_ROOTS" value="true" />
<option name="ADD_SOURCE_ROOTS" value="true" />
<option name="SCRIPT_NAME" value="$PROJECT_DIR$/deprecated/scrape2.py" />
<option name="PARAMETERS" value="" />
<option name="SHOW_COMMAND_LINE" value="false" />
<option name="EMULATE_TERMINAL" value="false" />
<option name="MODULE_MODE" value="false" />
<option name="REDIRECT_INPUT" value="false" />
<option name="INPUT_FILE" value="" />
<method v="2" />
</configuration>
...
You can see the environment variables are defined inside envs.
You can pass a externally defined environment variable using ${ENVNAME}. See below thread on SO
How to pass an environment variable as a command line parameter in Run/Debug configuration in PyCharm?