The uncertainty quantification is crucial to the high-precision prediction of composites’ effective properties. However, the unclear input uncertainties of multiscale parameters, complex uncertainty propagations of inter-scale correlations, and unaffordable computational cost of massive simulations are three primary problems at present. In this work, an innovative model with high accuracy and feasible cost for the mechanical property prediction of plain woven composites is developed encompassing minimum-size unit cells and multi-scale uncertainty quantification. For the accuracy holding, an uncertainty analysis process consists of the traceability description, inter-scale propagation and quantification is established. The uncertainties of geometry are described by uniform distributions for fiber, fiber bundle and composite scales, respectively; that of constituent properties is described by normal distributions for fiber and matrix, and its propagations to bundle and composite scales are realized by Nataf transformation methods with the consideration of parameter correlations. For the cost control, minimum-size unit cells are formulated by exhaustive analysis of structural symmetries to reduce the computational cost without accuracy compromising for the single simulation, and 1/8 and 1/16 unit cells compared with traditional full-size ones are obtained. The evolution convergence for statistical uncertainties of effective properties is finally obtained with totally reduced computational cost of 89%.