A novel metastable polymorph and an unstable amorphous phase of methoxyflavone were discovered after a decade since the first report of the X-ray crystal structure of this bioactive compound. The new polymorph (form B) was crystallized from a single solvent that produced two different polymorphs concomitantly, which is different from the reported structure of form A (CCDC code: FATYOP). The two polymorphs crystallized in the same P2₁/c space group, the asymmetric units in form A contain one and form B contains two molecules with different conformations. The conformational differences and the weak C–H⋯O intermolecular interactions played a major role in generating the methoxyflavone polymorphs. The polymorphs were characterized by X-ray diffraction, differential scanning calorimetry and FT-IR spectroscopy. Thermodynamic properties were unambiguously established using room-temperature competitive slurry experiments, solid-state milling and heating. Form A was more stable than form B, the amorphous phase was unstable and easily converted to form A at room temperature in 30 minutes. Form A had higher absorption area, the C_max and AUC of form A were approximately two times those of form B.