DATA_CONSISTENCY_CHECK is On in my table. I'm trying to check data consistency for audit purpose.When I update same value in the main table, the temporal table keeps history of the same row, which causes difficult to track the version changes.I'm using MSSQL server.
You misunderstood the function of DATA_CONSISTENCY_CHECK option. It's used to check if time ranges definded by system_start_time_column_name and system_end_time_column_name columns in PERIOD FOR SYSTEM_TIME do not overlap in base and historical table when you enable the link between the base and historical table ( this done when you execute CREATE/ALTER TABLE command).
If you need data deduplication in historical table you have to implement it yourself. It can be a maintenance task which disable the link, remove duplicates, update the time range columns correctely and enable link between base and historical table back.