The utilization of pen shell (Atrina pectinata) generally in some areas only as edible portion adductor muscle (meat) so the shells become fishery waste. Shells are raw materials that contain chitin and chitosan. Benefits of chitin and chitosan in various fields of modern industry are quite a lot, including in the pharmaceutical industry, biochemistry, biotechnology, biomedical, food, nutrition, paper, textile, agriculture, cosmetics, and healthcare membrane. Quality of chitosan is influenced by deacetylation degree which is one of the most important chemical characteristics. Deacetylation degree gives affect in application of chitosan, due to the value of amina chain and used to differentiate between chitin and chitosan. Deacetylation degrees of chitosan are determined by several factors such as NaOH concentration, temperature and time process. In addition, treatment of deacetylation process of chitin can give effect to deacetylation degree value of chitosan. The method that was used in this research was an experimental method with a statistical analysis of the data. The results showed that stage deacetylation process of chitin have the effect to increase deacetylation degree of chitosan. Multistage deacetylation process of chitin with 3 stage process was capable to make the deacetylation degree on average 75% with 82.91% of solubility. The increase result of deacetylation degree of chitosan is directly proportional with the increase in solubility.