Flexible strain sensors prepared by self-sensing nanocomposites using polydimethylsiloxane (PDMS) as the matrix material and carbon nanotubes (CNTs) as the conductive filler have received widespread attention due to their structural flexibility, outstanding weatherability and biocompatibility. Nevertheless, the high sensitivity, stable signal output, and durability are still limited by the uniform dispersion of the CNTs inside. In this paper, a novel preparation method different from direct dispersion was explored, in which CNTs were assembled on the surface of polystyrene (PS) microspheres to assist in CNT dispersion during the self-deployment of microspheres arrays. The free CNTs acted as a bridge to connect the conductive microspheres in the orientation-3D conductive network, which were essential for forming abundant conductive pathways. As numerous conductive fillers were added to the system to enhance conductivity, the self-alignment effect of the microsphere arrays was significantly inhibited, and it failed to assist well in the dispersion. Therefore, the covalent bonding strategy was employed to improve the dispersion and construct strong interfacial interaction, providing impressive electrical conductivity, structural stability, and outstanding durability and thermal stability. The PDMS/PS-C/CNT-N composites prepared with aminated CNT (CNT-N) and carboxylated PS microspheres (PS-C) showed better performance in sensitivity, achieving a gauge factor of over 70, a wide sensing range of 0–124%, and fast response of 330 ms and fast recovery of 190 ms. The developed sensory film was used as an intelligent sensor to monitor traffic flow information. It has been proved that not only the vehicle configuration can be accurately identified, but also the speed can be precisely back-calculated. It opens up new territory to develop high-performance flexible strain sensors for accurate, long-term, and stable acquisition of traffic flow information.