The invention provides an image capturing system, an image capturing apparatus, a decoding apparatus and an image capturing method. An image capturing system includes a photoelectric conversion unit, a charge holding unit, a multiple sampling information setting unit, a multiple sampling unit, a conversion unit, and an image reconstruction unit. The photoelectric conversion unit converts optical signals received by a plurality of pixels to electric signals. The charge holding unit stores the electric signals and holds the electric signals as charge signals. The multiple sampling information setting unit sets multiple sampling information used for a multiple sampling process. The multiple sampling information includes first multiple sampling information and second multiple sampling information. The multiple sampling unit performs the multiple sampling process using the multiple sampling information and the charge signals so as to output signals. The conversion unit converts the output signals to digital signals. The image reconstruction unit generates reconstructed images using the digital signals and the multiple sampling information, and outputs the reconstructed images.