Accurate bee counting is important for colony monitoring, pollination assessment, and precision beekeeping, but manual counting and dense point annotation are labor-intensive. This study proposes M3DANet, a lightweight semi-supervised density regression network with a handheld edge deployment system for bee colony counting. A dataset containing 586 valid high-resolution images and 34,869 point annotations was constructed for training and evaluation. M3DANet uses the first seven stages of MobileNetV3-Large as the lightweight backbone and combines multi-scale context encoding, attention-guided low-level feature fusion, and teacher–student consistency learning with confidence masking and warm-up training. The 10%, 30%, and 50% labeled data settings refer to the proportions of labeled images in the training set, and the remaining training images are used as unlabeled data. Mean absolute error (MAE) and root mean square error (RMSE) are used as evaluation metrics. On the main dataset, M3DANet achieved MAE values of 9.937, 7.003, and 5.570 and RMSE values of 13.093, 9.387, and 7.620 under the 10%, 30%, and 50% settings, respectively, outperforming representative semi-supervised baselines. Under the fully supervised setting, it achieved an MAE of 5.201 and an RMSE of 6.989 with only 2.095 M parameters and 416.64 FPS, using 87.1% fewer parameters and running 17.7 times faster than CSRNet. Cross-species experiments confirmed its low-label generalization ability. Jetson Orin NX deployment achieved 65.75 ms/image inference latency and 10.44 FPS complete-pipeline throughput. These results show that M3DANet balances counting accuracy, annotation efficiency, generalization, and edge deployment practicality.