Hi Dr MD Panna Ali,
Your fly photos are a bit dark and hard to see clearly but I think you may have reared out some flies belonging to family Ephydridae. Quite possibly they are a species of Hydrellia, some of which are known to attack rice. See some info at the following webpage:
Dear MD Panna Ali
Your submission was sent to Russell Cox, Australian Museum, and he kindly sent this message:
The pupae and environmental images are great but the adult fly images are too poor to identify properly; if lighter, clearer, images of lateral, dorsal and ventral habitus views can be obtained I can take the identification further.
The double costal break, plumose arista, distinct lappet with bristle all signify family Ephydridae.
There are several pest species of this family associated with rice: Hydrellia griseola, Notiphila riparia and Notiphila sekiyai.
It is definitely not Atherigona: Muscidae, which is a pest species on the shoots (not roots) of rice.