The Uncertainty-based Multidisciplinary Design Optimization (UMDO) method was studied for the conceptual design of fractionated modularized cluster spacecraft (fractionated spacecraft), so as to comprehensively assess and optimize life cycle cost, benefit, system robustness and flexibility under uncertainty. Firstly, the UMDO methodology was introduced, as well as the schematic flowchart of UMDO for the fractionated spacecraft conceptual design. Secondly, the system architecture and assessment criteria of the new concept fractionated spacecraft were explained. The disciplinary models, cost models and benefit models were described, and the uncertainties thereof were modeled with probability theory. Thirdly, a notional earth observatory fractionated spacecraft was used as an example to demonstrate the application of UMDO in the fractionated spacecraft conceptual design. The UMDO problem formulation and UMDO procedure organization were presented in detail. The results show that the mean of the net revenue and its robustness under uncertainty can be greatly improved, which verified the effectiveness of UMDO method for fractionated spacecraft conceptual design.