The synthesis, isomeric separation, and identification of β-sulphonic phthalocyanine zinc complexes were reported. While the sulphonic phthalocyanines have been studied extensively, the development of separation technology may enable deeper insights into their isomeric constitution. An ion-pair reversed-phase high performance liquid chromatography (IP-RP-HPLC) method was developed to separate the sulphonic phthalocyanine isomers. The results showed that the product of the condensation reaction is a mixture of all possible isomers with statistical distribution. Several isomers were obtained and structural determination was undertaken by NMR. Based on the IP-RP-HPLC elution sequence of these well-identified isomers, a relationship between the structure and efficiency was deduced: closely spaced intervals of sulphonic groups lead to higher hydrophobicity and shorter retention times on HPLC. Based on this relationship, each HPLC peak was assigned to the corresponding isomeric structure.