Hydroxyapatite (HA) is known to promote osteogenicity and enhance the mechanical properties of biopolymers. However, incorporating a large amount of HA into a porous biopolymer still remains a challenge. In the present work, a new method was developed to produce interconnected microporous poly(glycolic-co-lactic acid) (PLGA) with high HA nanoparticle loading. First, a ternary blend comprising PLGA/PS (polystyrene)/HA (40/40/20 wt%) was prepared by melt blending under conditions for formation of a co-continuous phase structure. Next, a dynamic annealing stage under small-strain oscillation was applied to the blend to facilitate nanoparticle redistribution. Finally, the PS phase was sacrificially extracted, leaving a porous matrix. The results from different characterizations suggested that the applied small-strain oscillation substantially accelerated the migration of HA nanoparticles during annealing from the PS phase to the PLGA phase; nearly all HA particles were uniformly presented in the PLGA phase after a short period of annealing. After dissolution of the PS phase, a PLGA material with interconnected microporous structure was successfully produced, with a high HA loading above 30 wt%. The mechanisms beneath the experimental observations, particularly on the enhanced particle migration process, were discussed, and strategies for producing highly particle loaded biopolymers with interconnected microporous structures were proposed.