Recent researches have shown that the relation between mitochondrial function and degenerative disorders is closely related to aging, such as Alzheimer's and Parkinson's diseases. Because these studies expose the need for detailed analysis of high-resolution physical alterations in mitochondria, three dimensional (3D) visualization of mitochondria from electron microscopy (EM) images is coming into prominence. To this end, how to develop suitable segmentation algorithms and connection algorithms has attracted our attentions. Since previous algorithms have shown preferable segmentation performance on mitochondria with different shapes and sizes. In this paper, we propose to utilize the segmentation information instead of detection information in context to obtain the mitochondrial connection relation in adjacent layers. Additionally, different from previous methods, we present a novel and effective connection approach by obtaining sparse matrixes and implementing a forward connection mode. Experiments on automated tape-collecting ultramicrotome scanning electron microscopy (ATUM-SEM) stacks demonstrate that our approach can effectively handle with the case of split and merge, and achieve a comparable connection quality measured by split error and merge error.