Does anyone knows how to import a flat file(comma delimited file) using data migrator with sql server as destination?

Yes. Do you have a master created for the flat file? If not, you'll need to do that first. Depending on how your flat file was created, a COMT, COM or DFIX master would probably be your best bet. I'm assuming you already have a data adapter and masters created to access your SQL Server tables. If not, do that too. Once that's done, just create your data flow as normal. If you've never created a Data Migrator data flow before, then I'd recommend you talk to your management about some training.