Wireless indoor localization has attracted significant amount of attention in recent years. Using received signal strength (RSS) obtained from WiFi access points (APs) for establishing fingerprinting database is a widely utilized method in indoor localization. However, the time-variant problem for indoor positioning systems is not well-investigated in existing literature. Compared to conventional static fingerprinting, the dynamicallyreconstructed database can adapt to a highly-changing environment, which achieves sustainability of localization accuracy. To deal with the time-varying issue, we propose a skeleton-assisted learning-based clustering localization (SALC) system, including RSS-oriented map-assisted clustering (ROMAC), cluster-based online database establishment (CODE), and cluster-scaled location estimation (CsLE). The SALC scheme jointly considers similarities from the skeleton-based shortest path (SSP) and the time-varying RSS measurements across the reference points (RPs). ROMAC clusters RPs into different feature sets and therefore selects suitable monitor points (MPs) for enhancing location estimation. Moreover, the CODE algorithm aims for establishing adaptive fingerprint database to alleviate the timevarying problem. Finally, CsLE is adopted to acquire the target position by leveraging the benefits of clustering information and estimated signal variations in order to rescale the weights fromweighted k-nearest neighbors (WkNN) method. Both simulation and experimental results demonstrate that the proposed SALC system can effectively reconstruct the fingerprint database with an enhanced location estimation accuracy, which outperforms the other existing schemes in the open literature.