Database size increased when I delete huge data

[Takashi Horita]

I have a problem when I delete huge data.

Situation:
I use contents management system to manage our contents. The system use MySQL as a database.

Problem:
Database size has increased when I had deleted over 300,000 contents. I made javascript program and delete contents via Rest API. I don't have knowledge to operate SQL databae, so I made javascript program and operate database via Rest API.
Database size has increased from 1.8GB to 7GB. I checked what file has increased. A file "/var/lib/mysql/ibdata1" has increased.

What I want to do:
I want to modify the javascript program that use Rest API or change MySQL settings so that database size will not increase. But I don't know how I can do it.

If someone know the solution, could you tell me the solution?