Graphene can find great potential applications in the future electronic devices. In bilayer graphene, the relative rotation angle between graphene layers can modulate the interlayer interaction and hence induces rich physical phenomena. We systematically study the temperature dependent magnetoresistance (MR) properties in the epitaxial bilayer graphene (BLG) grown on the SiC substrate. High quality BLG is synthesized by molecular beam epitaxy in ultra-high vacuum. We observe the negative MR under a small magnetic field applied perpendicularly at temperature < 80 K, which is attributed to a weak localization effect. The weak localization effect in our epitaxial BLG is stronger than previously reported ones in epitaxial monolayer and multilayer graphene system, which is possibly because of the enhanced interlayer electron transition and thus the enhanced valley scattering in the BLG. As the magnetic field increases, the MR exhibits a classical Lorentz MR behavior. Moreover, we observe a linear magnetoresistance behavior in a large field, which shows no saturation for the magnetic field of up to 9 T. In order to further investigate the negative and linear magnetoresistance, we conduct angle-dependent magnetoresistance measurements, which indicates the two-dimensional magnetotransport phenomenon. We also find that the negative MR phenomenon occurs under a parallel magnetic field, which may correspond to the moiré pattern induced local lattice fluctuation as demonstrated by scanning tunneling microscopy measurement on an atomic scale. Our work paves the way for investigating the intrinsic properties of epitaxial BLG under various conditions.