Conventional　asphalt　binder　derived　from　the　petroleum　refining　process　is　widely　used　in　pavement　engineering.　However,　asphalt　binder　is　a　non-renewable　material.　Therefore,　the　use　of　a　co-production　of　renewable　bio-oil　as　a　modifier　for　petroleum　asphalt　has　recently　been　getting　more　attention　in　the　pavement　field　due　to　its　renewability　and　its　optimization　for　conventional　petroleum-based　asphalt　binder.　Significant　research　efforts　have　been　done　that　mainly　focus　on　the　mechanical　properties　of　bio-asphalt　binder.　However,　there　is　still　a　lack　of　studies　describing　the　effects　of　the　co-production　on　performance　of　asphalt　binders　from　a　micro-scale　perspective　to　better　understand　the　fundamental　modification　mechanism.　In　this　study,　a　reasonable　molecular　structure　for　the　co-production　of　renewable　bio-oils　is　created　based　on　previous　research　findings　and　the　observed　functional　groups　from　Fourier-transform　infrared　spectroscopy　tests,　which　are　fundamental　and　critical　for　establishing　the　molecular　model　of　bio-asphalt　binder　with　various　biomaterials　contents.　Molecular　simulation　shows　that　the　increase　of　biomaterial　content　causes　the　decrease　of　cohesion　energy　density,　which　can　be　related　to　the　observed　decrease　of　dynamic　modulus.　Additionally,　a　parameter　of　Flexibility　Index　is　employed　to　characterize　the　ability　of　asphalt　binder　to　resist　deformation　under　oscillatory　loading　accurately.