Original model has 625153 cells and 689325 vertics. I want to modify model so I delect some cells and made some cells. Now, model has same cells as original model. But it has different vertics(885283 vertics) Isn't it Problem??

may be you have vertices defined twice. they can cause trouble, so try vmerg. another point: when you delete cells, the vertices are still there, so you probably have some unused vertices which do not cause any trouble, so don't worry about that.