Usually we take the direction of current opposite to the flow of charges. But in calculating the magnetic force, why do we consider the direction of current in the direction of movement of charges??

It is not the case in magnetic force too.

 

If a positive charge is moving, which is generally the case considered for convention, then the direction of current is taken as the direction of flow of charge.

 

However, if a negative charge is moving, then the direction of current is taken opposite to the direction of flow of charge.