Ni-rich nanodomains and Ti3Ni4 nanoprecipitates in the strain glass of Ni-rich Ti-Ni shape memory alloys (SMAs) play an important role in the origin and characteristic control of the strain glass transition. Ni-rich nanodomains are formed in the quenching process and dissolve during isothermal aging. Ti3Ni4 nanoprecipitates nucleate, grow and coarsen during aging. This study performed in situ small-angle X-ray scattering (SAXS) and ex situ X-ray diffraction to investigate the structural evolutions with aging time of nanoparticles in Ti48.7Ni51.3 SMA aged isothermally at 250 °C in terms of relative volume fraction, radius, thickness, orientation, lattice ordering, and morphology. The mechanism and kinetics of the concurrent phase evolutions of Ni-rich nanodomains and Ti3Ni4 nanoprecipitates are revealed and discussed in detail. Frequency-dependent storage modulus vs. temperature at different frequencies for different aging times was measured to characterize the strain glass transition. Quantitative correlation of all structural evolutions and kinetics of Ni-rich and Ti3Ni4 nanoparticles with respect to the variation and loss of the strain glass transition during aging times of 0 to 20 h is presented. The roles of different nanoparticles in causing or suppressing the strain glass behavior are also experimentally revealed.