Data imputation has been extensively explored to solve the missing data problem. The dramatically increasing volume of incomplete data makes the imputation models computationally infeasible in many real-life applications. In this paper, we propose an effective scalable imputation system named SCIS to significantly speed up the training of the differentiable generative adversarial imputation models under accuracyguarantees for large-scale incomplete data. SCIS consists of two modules, differentiable imputation modeling (DIM) and sample size estimation (SSE). DIM leverages a new masking Sinkhorn divergence function to make an arbitrary generative adversarial imputation model differentiable, while for such a differentiable imputation model, SSE can estimate an appropriate sample size to ensure the user-specified imputation accuracy of the final model. Extensive experiments upon several real-life large-scale datasets demonstrate that, our proposed system can accelerate the generative adversarial model training by 7.1x. Using around 7.6% samples, SCIS yields competitive accuracy with the stateof-the-art imputation methods in much shorter computation time.Index Terms-Data imputation, generative adversarial network, differentiable model, large-scale incomplete data 1 The support of a distribution is the complement of the largest open set of the random variables having zero-probability.