The origin of agate is distributed worldwide, and the mineralogical and spectroscopic characteristics of agates in most areas at home and abroad have been well studied. However, little research has been focused on the spectral characteristics and origin characteristics of agates from Madagascar. The banded structure and spectral characteristics of five agate samples from Antsohihy and Mahajanga were analyzed using polarization microscope, infrared spectrometer, and Raman spectrometer. The main mineral compositions of the samples from Mahajanga and Antsohihy are the same, which include α-quartz and moganite. The absence of characteristic Raman peaks (501 cm^-1) of white and red moganite near the center of the sample from Mahajanga, combining with the previous studies, is related to the dehydration reaction between structural water in the agate to form neutral water molecules, which react with moganite to form the quartz particles. However, the secondary minerals from those two areas are different. The Raman peaks of the agate from Mahajanga are 222, 294, 410, 1 316 cm^-1, which are proved to be hematite. But the Raman peaks of the samples from Antsohihy are 400~1 160 cm^-1.Therefore the secondary mineral is feroxyhyte. The impurity minerals in some samples from Antsohihy were proved to be α-quartz (moganite) and feroxyhyte by Raman spectrometer.It was speculated that four agates from Antsohihy were formed in a low-temperature (<80 ℃) environment with less Fe²⁺ content (β<0.03) and poor ventilation of air. Infrared spectrum test of agates from these two areas found that there were infrared characteristic peaks of liquid water (about 3 400 cm^-1) and structural water (3 750~3 500 cm^-1), the structural water (3 740 cm^-1) in agates from Antsohihy was proved to be located at structural defects. It is of great significance to speculate the formation mechanism of Madagascar agates by combining with the texture and spectral characteristics of Madagascar agates. Moreover, feroxyhyte can be used as a common mineral which is different from other producing areas and has the significance of producing areas. It also provides support for studying the geological environment of the formation of Madagascar agates.