In recent decades with increasing of global economic competition, small and medium scale industrials (SMEs) have known as an economic growth engine and a tool for employment. Therefore, they have important role in growth and development of countries. In order that these firms can compete in the world and they use the advantages of information technology requires infrastructures which provides electronic in various areas such as reducing transaction costs, develop marketing areas and access to markets, participate with suppliers and other partners. This paper is investigating effective organizational factor on implementing E-Commerce in SMEs. Primary data collected from questionnaire and has been analyzed through using SPSS software. The results of this study indicate that among technical, Social-Cultural, Managerial, human resource and logical factors, Managerial factors has important effect on Implementing E-Commerce