If I have to load multiple flat file say 3 file each with different structure into SQL database .Should I create 3 different flat file connection manager in ssis?
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Yes.
A Flat File Connection manager provides the contract between the shape of the source data and the reader component within your Data Flow Task.
The exact file name and the path to find said file can be changed on the fly during execution. But an additional/missing column, will cause the data flow to fail validation and the package will blow up.
If you had two files with the exact same layout but they served different purposes, I'd encourage you to make separate connection managers just to avoid complications - DistributorSales vs RetailSales. It might have the same columns (date, amount, item, purchaser) but the type of file implies an additional data point.