Di-perylene-3,4,9,10-tetracarboxylic acid bisimides (diPBI) is an n-type graphene molecule with nonplanar conformation. The controllable assembly and molecular adlayer structures of tetrachlorinated diPBI derivatives with different alkyl chains substitutions on highly oriented pyrolytic graphite were studied by scanning tunneling microscopy. When the molecule was substituted by butyl, the formation of multilayer or monolayer can be regulated by the solution concentration. When the molecule was substituted by 2-ethylhexyl, however, it can only form monolayer assembly. The unit cell of 2-ethylhexyl substituted diPBI adlayer was expanded to a rectangular shape compared to that of the butyl substituted diPBI. The steric repulsion of the alkyl chains (straight or branched) substitution is proposed as the key factor to control the adlayer structures of diPBI derivatives. The result is helpful to the design and fabrication of the organic film of chemically synthesized graphene type materials.