The positional effect of sulfonate groups on poly(butylene succinate) (PBS) microstructure was investigated. In this regard, unsaturated poly(butylene fumarate) (PBF) and poly(butylene succinate‐ran‐fumarate) copolymers, synthesized via esterification/polycondensation reactions, were modified through post‐polymerization modification. The progress of the PBF sulfonation reaction was analyzed via 1H NMR, dynamic light scattering and field emission SEM. The microstructure and thermal behavior of the functional polyesters were studied through DSC, TGA, elemental analysis and 1H NMR. Based on the results, the sulfonation reaction of unsaturated polymer chains, which are not experiencing a phase separation, is instantaneous, but sulfonation of the chains that have formed colloidal particles is a time‐consuming process. Surprisingly, the outcomes of 1H NMR analysis revealed a kind of heterogeneity along the fully sulfonated PBS backbone, similar to what is usually observed for copolymers. This is due to the ability of sulfonate groups to locate in different sites and create various block types. Due to the attraction between sulfonate groups, they tend to attach to the chain such that they provide the greatest number of second type blocks (containing two sulfonate groups). The randomness of sulfonated polymers after the sulfonation reaction was increased compared to that of the corresponding unsaturated copolymers. Increasing the content of sulfonate groups also led to a significant decrease in the thermal resistance (ca 120 °C) and crystallinity, along with a dramatic increase in ash content and Tg (up to 156 °C). © 2018 Society of Chemical Industry