How to Update more than 1 Row of the Table Through Storedprocedure

"Not working" can mean alot of things.
Let's start at the top:

select @Tot=count(*) from Pl_Material_Stock_Closing_Daily where MSLId=@MSLId and E_date>@E_date

Have you verified that this is returning a count that is greater than 0? If it is not, then you will never enter the while loop.

Now lets look at the select statement:

select @Id=A.MSLId from Pl_Material_Stock_Closing_Daily A where A.MSLId=(select Min(MSLId) from Pl_Material_Stock_Closing_Daily where MSLId=@MSLId and MSLId>@Id)

Here, the sub-query can only return the MSLID if it is equal to the variable @MSLId and greater than the variable @Id because of the where clause. MIN() is meaningless (because of the MSLId=@MSLId), but it implies that you are intending to do something different than what you have done. An equivalent statement is:

SELECT @Id=MSLId FROM P1_Material_Stock_Daily WHERE MSLId=@MSLId AND MSLId>@ID

Can you see the circular reference between Pl_Material_Stock_Closing_Daily.MSLId, @MSLId, and @Id?

And at the bottom:

UPDATE Pl_Material_Stock_Closing_Daily set QtyS = QtyS+@QtyS where MSLId=@Id and E_date=@E_date

This UPDATE is outside the while loop so it will not be updating on each iteration as you indicated you needed it to.

You may need to give us a better idea what you are trying to accomplish and a better understanding of what "not working" means if you want to fix this code.

Dear Sir, I have tryed your modified Code,I also Edit according to my Requrement,but it is not working.I think procedure is correct,it is Inside the LOOP,but where Condition is not satisfied,so output is : (0 row(s) affected).As I try to UPDATE the Rows which is > E_date of that MSLId (Rows may be 0/1/>1).I am giving complete StoredProcedure.[Is there process to check row by row in StoredProcedure like .NET(Break Point)]

Alter procedure [dbo].[sp_Ins_Up_TestIF]
(
@MSLId int,
@QtyS decimal,
@TDate varchar(50),
@E_date datetime,
@CC varchar(50),
@U_ID uniqueidentifier,
@Br_ID uniqueidentifier
)
as
declare @Q decimal, @I int,@Id datetime,@Tot int
begin

update Pl_Material_Stock_Level set Qty=Qty+@QtyS where MSLId =@MSLId
IF NOT EXISTS(select MSLId from Pl_Material_Stock_Closing_Daily where MSLId=@MSLId and E_date=@E_date)
BEGIN
select top 1 @Q=QtyS from Pl_Material_Stock_Closing_Daily where MSLId=@MSLId and E_date<@E_date order by E_Date desc
set @Q= @Q + @QtyS
insert into Pl_Material_Stock_Closing_Daily(MSLId,QtyS,TDate,E_date,CC,U_ID,BR_ID) values ( @MSLId,@Q,@TDate,@E_date,@CC,@U_ID,@Br_ID)
IF EXISTS(select MSLId from Pl_Material_Stock_Closing_Daily where MSLId=@MSLId and E_date>@E_date)
SELECT @Tot= COUNT(*) FROM Pl_Material_Stock_Closing_Daily WHERE MSLId=@MSLId AND E_date > @E_date
set @I = 0
WHILE(@I < @Tot)
BEGIN
SELECT @Id=A.E_date FROM Pl_Material_Stock_Closing_Daily A WHERE A.E_date = (SELECT Min(E_date) FROM Pl_Material_Stock_Closing_Daily WHERE MSLId=@MSLId and E_date>@Id)
SELECT @Id=E_date FROM Pl_Material_Stock_Closing_Daily WHERE MSLId=@MSLId AND E_date>@ID
UPDATE Pl_Material_Stock_Closing_Daily SET QtyS = QtyS + @QtyS WHERE MSLId=@MSLId and E_date=@Id
SET @I = @I + 1
END
END
ELSE
begin
UPDATE Pl_Material_Stock_Closing_Daily set QtyS = QtyS+@QtyS where MSLId=@MSLId and E_date=@E_date
IF EXISTS(select MSLId from Pl_Material_Stock_Closing_Daily where MSLId=@MSLId and E_date>@E_date)
SELECT @Tot= COUNT(*) FROM Pl_Material_Stock_Closing_Daily WHERE MSLId=@MSLId AND E_date > @E_date
set @I = 0
WHILE(@I < @Tot)
BEGIN
SELECT @Id=A.E_date FROM Pl_Material_Stock_Closing_Daily A WHERE A.E_date = (SELECT Min(E_date) FROM Pl_Material_Stock_Closing_Daily WHERE MSLId=@MSLId and E_date>@Id)
SELECT @Id=E_date FROM Pl_Material_Stock_Closing_Daily WHERE MSLId=@MSLId AND E_date>@ID
UPDATE Pl_Material_Stock_Closing_Daily SET QtyS = QtyS + @QtyS WHERE MSLId=@MSLId and E_date=@Id
SET @I = @I + 1
END
END
End