Yes
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table A contains around 100000 rows, table B contains 10000 rows, but Oracle use FK_A_TO_C index to gather 1041617280 rows, and it takes 1184298365/1000000=1184 seconds, why Oracle is doing this? Should I add /*+ INDEX(A PK_A) */ hint to MERGE statement to force it to use PK_A or use a stored outline?
Yes, it could help you. But need to be tested. Some times oracle picks wrong indexes, reason could be insufficient stats or bind variable...