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This paper proposes a novel Squeeze-and-excitation-based Mask Region Convolutional Neural Network (SEM-RCNN) for Environmental Microorganisms (EM) detection tasks. Mask RCNN, one of the most applied object detection models, uses ResNet for feature extraction. However, ResNet cannot combine the features of different image channels. To further optimize the feature extraction ability of the network, SEM-RCNN is proposed to combine the different features extracted by SENet and ResNet. The addition of SENet can allocate weight information when extracting features and increase the proportion of useful information. SEM-RCNN achieves a mean average precision (mAP) of 0.511 on EMDS-6. We further apply SEM-RCNN for blood-cell detection tasks on an open source database (more than 17,000 microscopic images of blood cells) to verify the robustness and transferability of the proposed model. By comparing with other detectors based on deep learning, we demonstrate the superiority of SEM-RCNN in EM detection tasks. All experimental results show that the proposed SEM-RCNN exhibits excellent performances in EM detection.