To investigate the rheological properties and influence mechanisms of twin-screw activated rubber composite-modified asphalt, we used SBS-modified asphalt (SBS) as the reference. Raw rubber powder composite-modified asphalt (RA/SBS) and activated rubber composite-modified asphalt (ARA/SBS) were prepared. A dynamic shear rheometer (DSR) and bending beam rheometer (BBR) were employed to comparatively analyze the rheological characteristics of the three modified asphalts, while Fourier transform infrared spectroscopy (FTIR) and fluorescence microscopy were used to reveal the micro-mechanisms in ARA/SBS. The results showed that ARA/SBS exhibited better storage stability and low-temperature flexibility compared to SBS and RA/SBS, and ARA/SBS demonstrated lower viscosity than RA/SBS. Among the three, ARA/SBS showed significantly improved high-temperature performance. The comparison of creep stiffness S and creep rate m indicated optimal performance in ARA/SBS, confirming that twin-screw activated rubber powder could significantly enhance the low-temperature properties of modified asphalt. Microscopically, chemical reactions occurred between oxygen-containing functional groups in activated rubber and polar groups in asphalt, while a cross-linked network structure formed between activated rubber molecules and asphalt molecular chains, improving compatibility and enhancing the rheological properties of composite modified asphalt.