The invention relates to an array multispectral optical filter and a manufacturing method thereof, belongs to the field of a micro-nano optical filter and solves the problem of integration of multichannel array detection in an existing nanofluidic chip. The optical filter only comprises the following four layers of structures: a two-dimensional metal grating layer, a buffer layer, a waveguide layer and a substrate. The invention also provides the manufacturing method of the optical filter, which utilizes a guided mode resonance principle of a two-dimensional metal grating and implements selection of different wavelengths by regulating the period of the grating. By the thickness of the buffer layer, the half-wave bandwidth of the cut-off wavelength also can be regulated. By regulating a suitable duty cycle of the two-dimensional metal grating layer, side lobes can be reduced. Therefore, relative to other turnable optical filters, the array multispectral optical filter manufactured by the method disclosed by the invention has the outstanding advantages of simple structure, low side lobes, adjustability of the half-wave bandwidth, high transmittance, no relation with polarization and the like. After the optical fiber disclosed by the invention is adopted, the integration of the nanofluidic chip can be implemented.