Proper budgeting and cost control are essential efforts for a successful project. The task has been conventionally supported by sophisticated project cost estimation from a production perspective. However, from a transaction cost perspective, the alliance risks with inter-organizational partners in joint venture (JV) projects should always be considered for budgeting. Aiming to assess the risks of a JV project, this paper proposes a transaction cost incorporated budgeting model with multi-criteria utility analysis. A case study is presented to demonstrate the applications of the proposed model which would help project managers to identify a proper risk contingency for practical project budgeting in construction JVs. The rationale of estimating the alliance risks with different partners is also enhanced by the proposed model.