Several measurements and observations were performed to improve the quality of Japanese noodles made from wheat cultivated in Saitama Prefecture. First, water distribution in noodles during and after boiling was investigated using magnetic resonance imaging (MRI). Water diffusion from the surface to the core was quantitatively determined by quantifying water distribution in the noodles, using the calibration line of spin-spin relaxation time (T2) and moisture content in gelatinized flour gels. The slope of the force-displacement curve corresponded with the changes in water distribution. It is known that water distribution is an important factor in determining the texture of boiled noodles. Then, observations of the microstructure of boiled noodles were conducted using a fluorescence microscope. The degree of starch granule swelling and the structure of the gluten network differed depending on the location within the boiled noodle. Moreover, the effects of flour type on microstructure were also observed on the noodle surface. With respect to noodle color preservation, loss of creamy/yellow color was observed in the boiled noodles made from high lutein content flour. The lipoxygenase activity remaining in the boiled noodles was thought to cause the discoloration, and the addition of antioxidant ingredients was effective in maintaining the color of boiled noodles.