The correlation between polymer microstructure of mPEG-PDLLA and secondary aggregation of its micelle was studied. Close examination of 1H NMR spectra revealed that the methine moieties, -CH(CH3)-, of mPEG-PDLLA polymer well represented its microstructure. To elucidate the physicochemical characteristics of various microstructures, we have developed an index, called L-ratio, to indicate the relative content of heterotactic component within the polymer. Storage stability of micelles from six polymers with different L-ratios (L-ratio ranging from 28 to 33%) was studied at 30 °C and 50 °C, and changes in average particle size were monitored to evaluate their secondary aggregation. We have found that polymers with high L-ratio takes longer time to secondary aggregation of polymeric micelles to occur. The findings should provide insightful guidance in the development of polymeric micelles.