I killed DBCC CheckDB Job of 3TB Database which has been rolling back since 17 hours with 89 %.as i have checked that the SPID running with waittype EXECSYNC. Could we have any other way to clear this mess without restarting SQL Server
Restarting a server while something is rolling back, is almost always a bad idea. You may make things worse.
You don't say if you are using one of the repair options with DBCC CHECKDB if you are, it can complicate things even more.
It has been a few hours since the original question was posted, so things have probably either self corrected or gotten worse. Hopefully you have backups, that you will be able to use in the recovery, if things are not going well.
Some Related posts that may help
See Paul Randall's comments on DBCC CHECKDB. https://www.sqlskills.com/blogs/paul/the-curious-case-of-unstoppable-dbcc-checkdb/