Diabetic macular edema (DME) is a common disease of diabetic retinopathy (DR). Due to the infection of DME disease, many patients’ vision is lost. To cure DME eye disease, early detection and treatment are very important and vital steps. To automatically diagnosis DEM disease, several studies were developed by detection of the macula center which is dependent on optic disc (OD) location. In this paper, a novel features pre-training based model was proposed based on dense convolutional neural network (DCNN) to diagnose DME related disease. As a result, a computerize tool “DME-Deep” for detection of DME-based grading system was implemented through a new dense deep learning model and feature’s transfer learning approaches. This DCNN model was developed by adding new five convolutional and one dropout layers to the network. The DME-Deep system was tested on three different datasets, which obtained from online sources. To train the DCNN model for features learning, the 1650 retinal fundus images were utilized from the Hamilton HEI-MED, ISBI 2018 IDRiD and MESSIDOR datasets. On datasets, the DME-Deep achieved 91.2% of accuracy, 87.5% of sensitivity and 94.4% of specificity. Compare to obtain hand-crafted features, the automatic feature’ learning it provided favorable results. Hence, the experimental results also indicate that this DME-Deep system can automatically assist ophthalmologists in finding DEM eye-related disease.