Video Variational Autoencoder (VAE) encodes videos into a low-dimensional latent space, becoming a key component of most Latent Video Diffusion Models (LVDMs) to reduce model training costs. However, as the resolution and duration of generated videos increase, the encoding cost of Video VAEs becomes a limiting bottleneck in training LVDMs. Moreover, the block-wise inference method adopted by most LVDMs can lead to discontinuities of latent space when processing long-duration videos. The key to addressing the computational bottleneck lies in decomposing videos into distinct components and efficiently encoding the critical information. Wavelet transform can decompose videos into multiple frequency-domain components and improve the efficiency significantly, we thus propose Wavelet Flow VAE (WF-VAE), an autoencoder that leverages multi-level wavelet transform to facilitate low-frequency energy flow into latent representation. Furthermore, we introduce a method called Causal Cache, which maintains the integrity of latent space during block-wise inference. Compared to state-of-the-art video VAEs, WF-VAE demonstrates superior performance in both PSNR and LPIPS metrics, achieving 2× higher throughput and 4× lower memory consumption while maintaining competitive reconstruction quality. Our code and models will be released to inspire further research.