Perfluorooctanoic acid (PFOA), a wide spread environmental pollutant, was associated with developmental cardiotoxicity in chicken embryo, while the underlying molecular mechanism had not been fully elucidated. In the current study, 2 mg/kg (egg weight) PFOA and/or 100 mg/kg (egg weight) L-carnitine were exposed to embryonic day zero (ED0) chicken embryo via air cell injection, and then bone morphogenic protein 2 (BMP2) silencing lentivirus or BMP2 recombinant protein were introduced into ED2 embryo. Electrocardiography and histological methods were utilized to assess the cardiac function and morphology in hatchling chickens, respectively. Consistent with previous results, 2 mg/kg PFOA exposure at ED0 significantly elevated heart rate and thinned right ventricular wall in hatchling chickens, while L-carnitine co-treatment reverted such changes. BMP2 silencing induced very similar changes in hatchling chicken hearts as PFOA exposure, while co-exposure of recombinant BMP2 protein alleviated PFOA-induced changes. L-carnitine exposure alleviated the BMP2-silencing induced changes as well. Western blotting revealed that PFOA exposure enhanced BMP2 expression and suppressed pSMAD1 expression in ED15 chicken embryo hearts, while both changes were reverted by L-carnitine co-exposure. Furthermore, silencing of BMP2 significantly increased the expression level of PPAR alpha in ED15 chicken embryo hearts, while silencing of PPAR alpha did not have significant impact on BMP2 expression. In conclusion, BMP2/pSMAD1 signaling participates in the PFOA-induced developmental cardiotoxicity in chicken embryo, which is likely located upstream of PPAR alpha for this particular endpoint. Protection of BMP2 signaling might contribute to L-carnitine mediated protection against PFOA-induced developmental cardiotoxicity.