Several copper phthalocyanines (CuPcs) with different substituents were applied to cellulosic fibre for studying their photocatalytic activities by using stain decolourisation methods. Even though the molar quantity of each CuPc derivative on cotton fabric were controlled to be equivalent, there were great difference on their photocatalytic activities. Distinct extents of the CuPc molecules dissociated by the cellulosic medium, owing to different CuPc molecular structures, were observed via absorption spectroscopic analyses. Liquid chromatography-mass spectrometry (LC-MS) was employed to determine the molecular structures of the CuPcs. A novel elution profile, termed as “double-isocratic” method, was developed to separate the relatively complex mixtures of the CuPc compounds, to prevent interference against mass spectrometric detection by buffers and ion-pairing reagents. The stain decolourisation performance of CuPcs were also compared to one of the traditional photocatalysts, titanium dioxide (TiO2), under visible light. Stronger photocatalytic activity was exhibited by CuPc-functionalised cottons than the TiO2-coated cotton. The outcomes of this study can make contributions to aggregation and photocatalytic studies of phthalocyanines in cellulosic materials, as well as phthalocyanine chemistry and applications.