The thermal storage stability of styrene–butadiene–styrene tri-block copolymer modified bitumen (SBSPMB) is the key to avoid performance attenuation during storage and transportation in pavement engineering. However, existing evaluation index softening point difference within 48 h (ΔSP48) cannot effectively distinguish this attenuation of SBSPMB. Thus, conventional physical indexes, rheological properties, and micro-structure characteristics of SBSPMB during a 10-day storage were investigated in this research. Results showed that during long-term thermal storage under 163 °C for 10 days, penetration, ductility, softening point, recovery rate (R%), and anti-rutting factor (G*/sinδ) were decayed with storage time increasing. This outcome was ascribed to the phase separation of SBS, which mainly occurred after a 4-day storage. However, ΔSP48 after a 6-day storage met the specification requirements (i.e., below 2.5 °C). Thus, the attenuation degree of asphalt performance in field storage was not effectively characterized by ΔSP48 alone. Results from network strength (I) and SBS swelling degree tests revealed that the primary cause was SBS degradation and base asphalt aging. Moreover, conventional indexes, including penetration, ductility, and softening point, were used to build a prediction model for rheological properties after long-term storage using partial least squares regression model, which can effectively predict I, R, Jnr, G*/sinδ, and SBS amount. Correlation coefficient is above 0.8. G*/sinδ and I at the top and bottom storage locations had high coefficient with SBS amount. Thus, phase separation of SBSPMB should be evaluated during thermal storage.