Two stereocomplexes (SCs) with different molecular weights in poly(L-lactide) (PLLA-49k and PLLA-163k) were prepared by mixing equal amounts of poly(D-lactide) (PDLA) and PLLA via the solution method. The exclusive formation of SCs was achieved in SC-PLLA-49k, whereas both homocrystallites (HCs) and SCs were observed in SC-PLLA-163k. Two blends were subjected to further processing via the ultrasonic microinjection molding technique at varying mold temperatures, yielding amorphous samples. As the samples were heated, the heating induced structural reorganization occurs with the concurrent SCs and HCs for all samples at ca. 80 °C. The degree of crystallinity for HCs XHC exhibits a positive correlation with the mold temperature, whereas the degree of crystallinity for SCs XSC shows a negative dependence on mold temperature for both systems. This behavior can be tentatively explained as follows. Firstly, the demixing of enantiomeric PLA chains occurs in the melt state as evidenced by twice heating measurements of blends. The degree of chain segregation is expected to increase with the increase in mold temperature due to lower supercooling, resulting in a decrease of PLLA/PDLA clusters (SC nuclei). Secondly, a high mold temperature is beneficial for the formation of HC nuclei as the chain mobility is improved. The reformulation of SC nuclei is difficult because of a longer diffusion distance required for PLA molecules. The coexistence of SC and HC nuclei causes the simultaneous appearance of SCs and HCs during heating of samples. As HCs start to melt, a transition from HCs to SCs occurs accompanied by a continuous increase in XSC. For both systems, a maximum of XSC is reached when SCs begin to melt followed by a mold temperature independent evolution of XSC upon further heating. Such a maximum is larger in the low molar mass system because it is less entangled. The reservation of SC nuclei is demonstrated by a comparison of the structural evolution and isothermal cold crystallization behavior between the two blends and their ultrasonic microinjection molded samples.