Diffusion Transformers (DiTs) have gained prominence for outstanding scalability and extraordinary performance in generative tasks. However, their considerable inference costs impede practical deployment. The feature cache mechanism, which involves storing and retrieving redundant computations across timesteps, holds promise for reducing per-step inference time in diffusion models. Most existing caching methods for DiT are manually designed. Although the learning-based approach attempts to optimize strategies adaptively, it suffers from discrepancies between training and inference, which hampers both the performance and acceleration ratio. Upon detailed analysis, we pinpoint that these discrepancies primarily stem from two aspects: (1) Prior Timestep Disregard, where training ignores the effect of cache usage at earlier timesteps, and (2) Objective Mismatch, where the training target (align predicted noise in each timestep) deviates from the goal of inference (generate the high-quality image). To alleviate these discrepancies, we propose HarmoniCa, a novel method that Harmonizes training and inference with a novel learning-based Caching framework built upon Step-Wise Denoising Training (SDT) and Image Error Proxy-Guided Objective (IEPO). Compared to the traditional training paradigm, the newly proposed SDT maintains the continuity of the denoising process, enabling the model to leverage information from prior timesteps during training, similar to the way it operates during inference. Furthermore, we design IEPO, which integrates an efficient proxy mechanism to approximate the final image error caused by reusing the cached feature. Therefore, IEPO helps balance final image quality and cache utilization, resolving the issue of training that only considers the impact of cache usage on the predicted output at each timestep.