The present invention relates to a polybutylene terephthalate (PBT) elastomer composition having excellent heat resistance, and more particularly to a polybutylene terephthalate (PBT) elastomer composition comprising: a PBT resin; a vegetable oil or an environmentally friendly plasticizer, which serves to reduce the hardness of the PBT resin; a glycol-modified polyethylene terephthalate (PET-G) resin and a thermoplastic polyester elastomer (TPEE) resin, which serve to improve physical properties and processability; and a core-shell type copolymer having excellent miscibility with the plasticizer. In a preferred embodiment, the PBT elastomer composition comprises: 100 parts by weight of a PBT resin; 10 to 120 parts by weight of an environmentally friendly plasticizer; and 10 to 120 parts by weight of a thermoplastic copolyester elastomer (TPEE) resin.