Yes it is possible to have different theme for different store.
Copy the theme which you have already created and paste again in the app/design directory and rename the theme directory and the changes you wanted to make in css file.
Now go to the Content -> Design -> configuration -> Over there you will see all the stores and the websites you have created -> just select your second theme for second store
Click on save button.
Run below commands :
php bin/magento indexer:reindex
php bin/magento cache:clean
php bin/magento cache:flush
Then check it will works !
if issue solved,Click Kudos & Accept as Solution