The morphology and properties of polyamide 6 (PA6)/poly(butylene terephthalate) (PBT) blends filled by three types of glass fibers (GF) with different surface properties were investigated. The GF were unmodified or surface-modified for PA6 or PBT, denoted as GF(Pris), GF(PA6), and GF(PBT), respectively. The incorporation of 15 wt % of GF with different surface properties all led to a transition from a cocontinuous (at least a part of each phase penetrates the whole volume in a coherent and continuous manner) to a sea-island (separated domains dispersed in a continuous matrix) morphology with PA6 being the matrix phase when PA6/PBT equaled 45/55. GF(Pris) was always encapsulated by PA6, while the encapsulating layers on the surfaces of GF(PA6) and GF(PBT) changed from PBT to PA6 with increasing PA6 contents. The morphological changes induced by GF caused more PBT to crystallize at a lower temperature and enhanced the alkali tolerance of the blend significantly.