Law Number 21 of 2001 concerning Special Autonomy for the Papua Province is a shortcut to solving problems in Papua. The enactment of Law Number 21 of 2001 has made Papua Province as a region that has special authority to regulate and manage its own region. The special authority granted to the province of Papua is characterized by culture and customs. Law Number 21 of 2001 has a major influence on the organizational structure of local government in the Province of Papua. The implementation of special autonomy in the Province of Papua to improve the welfare of the Papuan people based on the basic rights of the Papuan People and make the Papua Province equal with other Provinces in Indonesia. Until now, the objectives of the special autonomy have not been fully achieved. The purpose of this study is to analyze the effect of special autonomy and also the factors that affect the effectiveness of the implementation of special autonomy by using normative legal research. The results of this study indicate that the provincial government does not manage the special autonomy of Papua well so that the implementation of regional government in the province of Papua based on special autonomy has not achieved its goal, that is to prosper the people of Papua.