Block ionomer complexes SSEBS-c-PCL were prepared, as a consequence of proton transfer from the sulfonic acid of sulfonated polystyrene-block- poly(ethylene-ran-butylene)-block-polystyrene (SSEBS) to the tertiary amine of a tertiary amine terminated poly(ε-caprolactone) (APCL). The phase behavior of SSEBS-c-PCL was thoroughly investigated and the results showed that APCL in SSEBS-c-PCL displays unique crystallization behavior owing to the influence of interactions between the amine and sulfonic acid groups as well as the effects of confinement. Further, small-angle X-ray scattering study revealed that SSEBS-c-PCL displays a less ordered micro-phase structure compared to SSEBS. A quantitative mapping of mechanical properties at the nanoscale was achieved using peak force mode atomic force microscopy. It is found that the block ionomer complex possesses a higher average elastic modulus after complexation with crystallizable APCL. Additionally, the moduli for both hard and soft phases increase and the phase with higher modulus assignable to the hard SPS component shows much more pronounced changes after complexation, confirming that APCL interacts mainly with the SPS blocks. This provides an understanding of the composition and nanomechanical properties of these new block ionomer complexes and an alternative insight into the micro-phase structures of multi-phase materials.