Reconstructing visual stimuli from brain recordings has been a meaningful and challenging task in brain decoding. Especially, the achievement of precise and controllable image reconstruction bears great significance in propelling the progress and utilization of brain-computer interfaces. Recent methods, leveraging advances in the power of text-to-image generation models, have reconstructed images that closely approximate complex natural stimuli in terms of semantics (e.g., concepts and objects). However, they struggle to maintain consistency with the original stimuli in fine-grained structural information (e.g., position, orientation and size), which undermines both the controllability and interpretability of the models. To address the aforementioned issues, we propose a two-stage image reconstruction framework, termed MindDiffuser. In Stage 1, Contrastive Language-Image Pretraining (CLIP) text embeddings decoded from brain responses are input into Stable Diffusion, generating a preliminary image containing semantic information. In Stage 2, we use decoded shallow CLIP visual features as supervisory signals, iteratively refining the feature vectors from Stage 1 via backpropagation to align structural information. We conducted extensive experiments on brain response datasets across three modalities (fMRI, EEG, MEG) elicited by visual stimuli, demonstrating that our framework significantly enhances the performance of previous state-of-the-art models, highlighting the effectiveness and versatility of our approach. Spatial and temporal visualization results further support the neurobiological plausibility of our framework, providing guidance for future neural decoding efforts across different brain signal modalities.