Popular transformer-based detectors detect objects in a one-to-one manner, where both the bounding box and category of each object are predicted only by the single query, leading to the box-sensitive category predictions. Additionally, the initialization of positional queries solely based on the predicted confidence scores or learnable embeddings neglects the significant spatial interrelation between different queries. This oversight leads to an imbalanced spatial distribution of queries (SDQ). In this paper, we propose a new MLP-DINO model to address these issues. Firstly, we present a new Query-Independent Category Supervision (QICS) approach for modeling categories information, decoupling the sensitive bounding box prediction process to improve the detection performance. Additionally, to further improve the category predictions, we introduce a deep MLP model into transformer-based detection framework to capture the long-range and short-range information simultaneously. Thirdly, to balance the SDQ, we design a novel Graph-based Query Selection (GQS) method that distributes each query point in a discrete manner by graphing the spatial information of queries to cover a broader range of potential objects, significantly enhancing the hit-rate of queries. Experimental results on COCO indicate that our MLP-DINO achieves 54.6% AP with only 44M parame ters under 36-epoch setting, greatly outperforming the original DINO by +3.7% AP with fewer parameters and FLOPs. The source codes will be available at https://github.com/Med-Process/MLP-DINO.