The booming e-commerce has played an important role in the growth of regional economy and the e-commerce of underdeveloped regions has been developing rapidly as well. However, there is a large gap between underdeveloped and developed regions due to the limitation of economic foundation, geographical condition and other factors. The research of effects on the e-commerce development of underdeveloped regions played an important role in the promotion of e-commerce. Based on the perspective of operating process, starting from the indicator of information flow, capital flow and logistics, this article established the indicator system of effects on e-commerce in underdeveloped region. After collecting data by questionnaire survey, getting the right of each index by AHP and comparing the differences of important indicators between the en-commerce developments in the eastern and western important indicators, summarize the factors which affect the e-commerce development of underdeveloped regions, proposes to suggestions such as strengthen the guide of government functions and so on.