env is the name of a Unix program. If you read the manual (man env) you can see that one way to use it is env COMMAND, where in your case, COMMAND is python3.
According to the manual, this will
Set each NAME to VALUE in the environment and run COMMAND.
Running env alone will show you what NAMEs and VALUEs are set:
$ env
TERM=xterm-256color
SHELL=/bin/bash
PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin
…
Therefore, /usr/bin/env python3 is an instruction to set the PATH (as well as all the other NAME+VALUE pairs), and then run python3, using the first directory in the PATH that contains the python3 executable.