To inhibit Thrombin (factor IIa) the heparin molecule has to bind to Anti-Thrombin III and Thrombin simultaneously.
The binding to to ATIII is via a high affinity penta-saccharide sequence while the binding to Thrombin is via additional 13 saccharides.
To inhibit factor Xa the heparin molecule need only the pentasaccharide sequence and no need for binding the Xa molecule.
Therefore, heparin molecules (less than 18 saccharides in length) i.e. LMW heparin will act more by inhibiting factor Xa than on thrombin (IIa).
Have a look at this illustration
click to enlarge
Image Referenced from <a href="http://chestjournal.chestpubs.org/content/119/1_suppl/64S.full">10.1378/chest.119.1_suppl.64S
CHEST January 2001 vol. 119 no. 1 suppl 64S-94S