SSISDB on AlwaysOn Group running package on Secondary Replica
... but when failing over to second replica, the jobs fails.
Asking to create master Key or certificate.

This is due to how security works with keys in SQL Server. There are various methods around this.

is there a way to automate this and whenever FaillOver happen the jobs should be running as they are on Primary replica?

For the first part, yes, see the second link above. For the second part, IMHO you shouldn't be executing any SSIS jobs on a SQL Server because they don't play well together in terms of sharing resources. Period. You're asking for performance issues when doing this and I'd stay far, far away from it.