Hello Li Jiyuan,
There is no difference opening a MODIS 1B file using File ->Open Image File or File ->Open External ->EOS->MODIS. Both options open the file in the exact same way. If I open the file in the first way and georeference it, then open it again in the second way and georeference it, my results are identical.
Are you actually using two different MODIS datasets, which may or may not mosaic together perfectly?
Another option you might consider is using the MODIS Toolkit available from the User Contribution site here:
http://www.ittvis.com/cod...k/search.asp?FID=485
This provides support for many other MODIS formats as well as 1B.