Recently, several studies (Zhou et al., 2021a; Zhang et al., 2021b; Kim et al., 2021; Zhou and Gu, 2022) have provided variance-dependent regret bounds for linear contextual bandits, which interpolates the regret for the worst-case regime and the deterministic reward regime. However, these algorithms are either computationally intractable or unable to handle unknown variance of the noise. In this paper, we present a novel solution to this open problem by proposing the first computationally efficient algorithm for linear bandits with heteroscedastic noise. Our algorithm is adaptive to the unknown variance of noise and achieves an $\tilde{O}(d \sqrt{\sum_{k = 1}^K σ_k^2} + d)$ regret, where $σ_k^2$ is the variance of the noise at the round $k$, $d$ is the dimension of the contexts and $K$ is the total number of rounds. Our results are based on an adaptive variance-aware confidence set enabled by a new Freedman-type concentration inequality for self-normalized martingales and a multi-layer structure to stratify the context vectors into different layers with different uniform upper bounds on the uncertainty. Furthermore, our approach can be extended to linear mixture Markov decision processes (MDPs) in reinforcement learning. We propose a variance-adaptive algorithm for linear mixture MDPs, which achieves a problem-dependent horizon-free regret bound that can gracefully reduce to a nearly constant regret for deterministic MDPs. Unlike existing nearly minimax optimal algorithms for linear mixture MDPs, our algorithm does not require explicit variance estimation of the transitional probabilities or the use of high-order moment estimators to attain horizon-free regret. We believe the techniques developed in this paper can have independent value for general online decision making problems.