Abstract: Data assimilation (DA) is an essential statistical technique for generating accurate estimates of a physical system's states by combining prior model predictions with observational data, especially in the realm of weather forecasting. Effectively modeling the prior distribution while adapting to diverse observational sources presents significant challenges for both traditional and neural network-based DA algorithms. This paper introduces VAE-Var, a novel neural network-based data assimilation algorithm aimed at 1) enhancing accuracy by capturing the non-Gaussian characteristics of the conditional background distribution $p(\mathbf{x}|\mathbf{x}_b)$, and 2) efficiently assimilating real-world observational data. VAE-Var utilizes a variational autoencoder to learn the background error distribution, with its decoder creating a variational cost function to optimize the analysis states. The advantages of VAE-Var include: 1) it maintains the framework of traditional variational assimilation, enabling it to accommodate various observation operators, particularly irregular observations; 2) it lessens the dependence on expert knowledge for constructing the background distribution, allowing for improved modeling of non-Gaussian structures; and 3) experimental results indicate that, when applied to the FengWu weather forecasting model, VAE-Var outperforms DiffDA and two traditional algorithms (interpolation and 3DVar) in terms of assimilation accuracy in sparse observational contexts, and is capable of assimilating real-world GDAS prepbufr observations over a year.