A series of six-membered sulfonated poly(imide-siloxane)s (SPIs) was synthesized using 1,4,5,8-naphthalenetetracarboxylic dianhydride (NTDA), aminopropyl-terminated polydimethylsiloxane (PDMS) 2,2-benzidinedisulfonic acid (BDSA), as the sulfonation target diamine groups, and various nonsulfonated diamine monomers behaving as bridging groups. The structure-property relationship of SPI-SXx membranes is discussed in detail according to the chemical structure of the various nonsulfonated diamines of the SPI-SXx membranes from the viewpoints of proton conductivity, ion exchange capacity (IEC), and membrane properties (water uptake and membrane swelling) at equal PDMS content SPI-SXx. The PDMS was introduced to enhance the proton conductivity and water uptake attributed from the high flexibility of the siloxane segments. The conductivity and water uptake of angled SPI-SXm and oxydianiline-based SPI-SX membranes (SPI-SXO) are greater than those prepared from diaminodiphenylmethane-based SPI-SX membranes (SPI-SXD) at a given IEC. These differences resulted from the increased number of entanglements of the SPI-SXx membrane. The SPI-SXD showed almost isotropically dimensional changes with the increase in water uptake, and the volume were slightly smaller than those estimated from the additivity rule. Free volume in the SPI-SXx increased with the increase in bulky irregular packing in nonsulfonated segments, which augmented the water uptake and, in turn, the conductivity of the polymer. With the increase in temperature, conductivity increased more rapidly in SPI-SXx than in Nafion 117. Microscopic analyses revealed that these smaller and well-dispersed hydrophilic domains contribute to better proton conducting properties. The new sulfonated poly(imide-siloxane)s have proved to be a possible candidate as the polymer electrolyte membrane for polymer electrolyte fuel cells (PEFCs) and direct methanol fuel cells (DMFCs).