Strategic alliances have become one of the most efficient governances to build competitive advantages in E-commerce industry. A strategic alliance is also regarded as a risky business which inter-organizational partners should always be considered. From professional investors to practitioners, they are concerned with risks from transaction cost perspective in strategic alliances. Therefore, risk identification and a systematic framework for risk assessment is important to assure the success of business practices with strategic alliances. This research proposes a framework that comprises risk factors and the analytical hierarchy for strategic alliances in E-commerce industry. To facilitate objective and systematic risk assessment, analytical hierarchy process (AHP) is proposed to calculate the weighted value each criteria for strategic alliances. Delphi questionnaire surveys were distributed to the respondents by AHP method. The data collection was conducted from experts of E-commerce companies and analyzed by Super Decision Software (ANP) version 2.2. The result of study presented five main factors effect to strategic alliance in E-commerce the most are: economic, quality, resource, project member and cost. Furthermore, with the proposed framework, managers would be guided to evaluate the risks involved in their E-commerce co-operations and consequently their managerial policies to the practices.