We investigated the effect of ionic component on crystalline morphology development during isothermal annealing in a sodium neutralized sulfonated poly(ethylene terephthalate) ionomer (Ion-PET) by time-resolved small-angle x-ray scattering (TR-SAX S) using synchrotron radiation. At early stage in Ion-PET, SAXS intensity at a low annealing temperature (Ta = 120 $^{circ}C)$ decreased monotonously with scattering angle for a while. Then SAXS profile showed a peak and the peak position progressively moved to wider angles with isothermal annealing time. Finally, the peak intensity decreased, shifting the peak angle to wider angle. It is revealed that ionic aggregates (multiplets structure) of several nm, calculated by Debye-Bueche plot, are formed at early stage. They seem to accelerate the crystallization rate and make fine crystallites without spherulite formation (supported by optical microscopy observation). From decrease of peak intensity in SAXS,it is suggested that new lamellae are inserted between the preformed lamellae so that the concentration of ionic multiplets in amorphous region decreases to lower the electron density difference between lamellar crystal and amorphous region. In addition, analysis on the annealing at a high temperature (Ta = 210 $^{circ}C)$ by optical microscopy, light scattering and transmission electron microscopy shows a formation of spherulite, no ionic aggregates, the retarded crystallization rate and a high level of lamellar orientation.