Attenuated total reflection Fourier transform infrared (ATR-FTIR) is a promising alternative to conventional transmission-FTIR. However, previous research has found that on evaluating the Styrene–Butadiene–Styrene-modified asphalt (SBSMA), ATR-FTIR and transmission-FTIR tend to have different conclusions. Due to the surface sensitivity of ATR-FTIR and varying morphology of SBSMA, ATR-FTIR may yield abnormal SBS infrared peak intensity growth upon aged SBSMA samples. In this paper, to further investigate how different SBS and sulphur dosages will influence the ATR-FTIR observation, conventional SBSMA (4.5%) and highly modified SBSMA (7.5%) were characterised using FTIR and fluorescence microscopy. It was found different SBS/sulphur dosages, and the application of laboratory ageing could notably vary the SBSMA morphology and therefore influence the obtained SBSMA infrared spectra. This phenomenon was more pronounced for highly modified SBSMA (7.5%) which had larger polymer particles.