NIR spectroscopic analysis was used for the measurement of deproteinization and deacetylation to apply the merits of NIR spectroscopic analysis to the quality management in the process of chitin and chitosan production. In measuring squid pen and red snow crab shell, which are raw materials of chitin and chitosan by NIR there were typical peaks in 1200 nm, 1510 nm, 2050 nm and 2180 nm. Squid pen had somewhat higher peak than red snow crab shell. In producing chitin, amount of protein was decreased. Measuring it by NIR, reduction of protein caused by deproteinization was identified in producing chitin. Chitosan is a derivative material made from chitin by processing the deacetylation. During this processing, acetyl groups were removed and amide bends were appeared. From NIR spectra, peaks at 1530 nm and 2030 nm indicated amide II peak of chitosan, and these peaks were used for identifying the differences of structure between chitin and chitosan. The error in measurement of nonidentified sample was below $1\%$ and the error in the standard curve was below 0.006. These errors were very low and the accuracy of NIR was considered to be superior to the existing methods.