If no one is playing content from your Plex Media Server and it’s the “Plex New Transcoder” process using your CPU, you’ve probably enabled video preview thumbnails generation.
Related Page: Why is Plex using lots of CPU when nothing is playing?
If that option is not enabled and you’re only seeing brief, occasional spikes, the most common cause of this would be when the Plex Media Server reads your iTunes library. This can occur when iTunes is playing music or other content on the same machine that’s running the Plex Media Server. In such a case, the iTunes library will occasionally be read to pickup changes in the library, which can cause a brief spike in CPU usage.