Simple way, but not recommended (modifing Docker’s files directly could lead to errors):
echo "" > $(docker inspect --format='{{.LogPath}}' <container_name_or_id>)
Instead, you can have Docker automatically rotate the logs for you. This is done with additional flags to dockerd if you are using the default JSON logging driver:
dockerd ... --log-opt max-size=10m --log-opt max-file=3