Due to some problems in the past, OnePlus has decided to develop their own operating system called OxygenOS and drop CyanogenMod that was available with OnePlus One. Although the OS doesn't come pre-installed, Cyanogen is still releasing it for OnePlus' phones.
If you are not a fan of OxygenOS, now you can install CyanogenMod 13 on OnePlus 3. Cyanogen has now released a nightly build for the handset, but be aware that the Dash Charge feature is not supported in CM13, so you will charge your phone a little longer. Another drawback is a little worse camera performance, since the latest processing software used in OxygenOS is not included.