The stochastic inverse problem (StocIP), which aims to align push-forward and observed output distributions by estimating probability distributions of unknown system inputs, often faces optimization challenges and the curse of dimensionality. A novel deep network called StocIPNet which comprises an affine-embedded reparameterization subnetwork (ReparNet) and a complex system metamodeling subnetwork (MetaNet) is proposed to alleviate these issues. The ReparNet subnetwork embeds the affine transformation to convert the statistical parameters of the physical random vector into learnable weights and biases, effectively implementing the reparameterization trick by separating random and deterministic elements in the stochastic sampling operation to preserve differentiability. In parallel, the MetaNet subnetwork offers a computationally efficient alternative to time-consuming forward solvers, facilitating the generation of push-forward distributions. The entire StocIPNet utilizes the kernel maximum mean discrepancy (MMD) as a distribution-free loss function, quantifying the discrepancy between push-forward and observed output distributions. By leveraging the ReparNet's advantage of reformulating the sampling process as a differentiable transformation and combining two subnetworks seamlessly, the StocIP is reconfigured into a pure network training paradigm preserving differentiability perfectly, which allows for direct modeling and efficient inference of uncertainty within the network using automatic differentiation, backpropagation and gradient-based optimization methods, enabling ease of scaling to high-dimensional problems. The proposed framework has been theoretically demonstrated to be equivalent to the maximum likelihood method, ensuring its solid probabilistic interpretable foundation. The proposed framework is applied to perform stochastic model updating on a numerical and an experimental structure, which effectively demonstrates the framework's remarkable effectiveness and high efficiency in treating high-dimensional StocIPs.