They have a dedicated section on their page for this ...
There are 3 ways: through environment variables, set the /conf volume and create a new image
The volume /conf probably matches the OP desire:
To make arbitrary configuration changes to Neo4j, provide a container with a volume of / conf.
docker run \ --detach \ --publish=7474:7474 --publish=7687:7687 \ --volume=$HOME/neo4j/data:/data \ --volume=$HOME/neo4j/logs:/logs \ --volume=$HOME/neo4j/conf:/conf \ neo4j:3.1
Any configuration files in the / conf volume will override the files provided by the image. This includes values that can be set in response to environment variables passed to the Docker container. Therefore, if you want to change one value in a file, you must make sure that the rest of the file is complete and correct.
To reset the original set of configuration files, run the image using the dump-config command.
docker run --rm\ --volume=$HOME/neo4j/conf:/conf \ neo4j:3.1 dump-config