Join Subquery result in Linq

Yes, you can join sub queries. Like this:

var query = from f in db.ApplicationFees
            join sub in (from p in db.Payments
                         where p.Type == 1 && p.Position == 1 && 
                               p.Date >= fromDate && p.Date <= toDate
                         group p by p.ApplicationNo into g
                         select new {
                              ApplicationNo = g.Key,
                              CNT = g.Count(),
                              AMNT = g.Sum(x => x.Amount)
                         }) 
           on f.ApplicationNo equals sub.ApplicationNo into feePayments
           select new { Fee = f, Payments = feePayments };

But writing it in single query is not very maintainable. Consider to compose your query from sub-queries defined separately:

var payments = from p in db.Payments
               where p.Type == 1 && p.Position == 1 && 
               p.Date >= fromDate && p.Date <= toDate
               group p by p.ApplicationNo into g
               select new {
                    ApplicationNo = g.Key,
                    CNT = g.Count(),
                    AMNT = g.Sum(x => x.Amount)
              };

var query = from f in db.ApplicationFees
            join p in payments 
               on f.ApplicationNo equals p.ApplicationNo into feePayments
            select new { Fee = f, Payments = feePayments };