With recent advances in building foundation models for texts and video data, there is a surge of interest in foundation models for time series. A family of models have been developed, utilizing a temporal auto-regressive generative Transformer architecture, whose effectiveness has been proven in Large Language Models. While the empirical results are promising, almost all existing time series foundation models have only been tested on well-curated ``benchmark'' datasets very similar to texts. However, real-world time series exhibit unique challenges, such as variable channel sizes across domains, missing values, and varying signal sampling intervals due to the multi-resolution nature of real-world data. Additionally, the uni-directional nature of temporally auto-regressive decoding limits the incorporation of domain knowledge, such as physical laws expressed as partial differential equations (PDEs). To address these challenges, we introduce the Time Diffusion Transformer (TimeDiT), a general foundation model for time series that employs a denoising diffusion paradigm instead of temporal auto-regressive generation. TimeDiT leverages the Transformer architecture to capture temporal dependencies and employs diffusion processes to generate high-quality candidate samples without imposing stringent assumptions on the target distribution via novel masking schemes and a channel alignment strategy. Furthermore, we propose a finetuning-free model editing strategy that allows the seamless integration of external knowledge during the sampling process without updating any model parameters. Extensive experiments conducted on a varity of tasks such as forecasting, imputation, and anomaly detection, demonstrate the effectiveness of TimeDiT.