Alkaline polymer electrolyte fuel cells (APEFCs) are a class of promising energy conversion devices that are attracting ever-growing attention from the academic and industrial energy technology communities. Considerable efforts have been made towards the development of advanced alkaline polymer electrolytes (APEs), and manipulating the balance between high ionic conductivity and low swelling degree is consistently one of the most important trade-offs in APE design. Constructing hydrophilic/hydrophobic microphase-separated morphologies in APEs has long been accepted as an effective way to optimize the ionic conductivity of these materials. However, not all patterns of phase separation lead to high APE ion conductive efficiency. Here we compare two kinds of polysulfone-based APE materials (i.e. self-aggregated quaternary ammonium polysulfone (aQAPSF) and pendant quaternary ammonium polysulfone (pQAPSF)). Experimental and simulation observations unambiguously reveal the existence of distinctly different patterns of microphase separation in aQAPSF and pQAPSF. In aQAPSF, the hydrophobic side chains residing apart from the quaternary ammonium (QA) group help to build broad and percolated pathways, which contribute to boosting the ion conductive efficiency of the material. The aQAPSF membrane with IEC equal to 0.98 mmol g⁻¹ shows ionic conductivity as high as 108.3 mS cm⁻¹ at 80 °C. While in pQAPSF, the introduction of a side chain between the backbone and the cation locates the QA group away from the backbone and helps to build strong hydrophobic networks, which results in limited development of efficient ionic channels. However, when doubling the IEC of pQAPSF to 2.04 mmol g⁻¹, the conductivity can be increased to 75.1 mS cm⁻¹ at 80 °C, and the hydrophobic network restrains the swelling of pQAPSF effectively (swelling degree is 25.0% at 80 °C). These materials with obvious phase separation showed good chemical stabilities, and can be considered competitive candidates for application in fuel cells.