The bone marrow is the major site of hematopoiesis in mammals. The bone marrow microenvironment has been the topic of increasing study over the last two decades, as it is now widely recognized that rare, diverse non-hematopoietic cells provide crucial signals and support which enable hematopoietic stem cell maintenance and function. There have been very few studies of the bone marrow microenvironment in humans. In this dissertation, I sought to address this knowledge gap by taking a systems biology approach. We developed a clinical collaboration to get fresh human femoral head samples from orthopedic surgeries. Then, we developed methods to isolate cells, performed single-cell RNA sequencing (scRNA-Seq), created an antibody panel and performed Co-Detection by Indexing multiplexed imaging (CODEX), analyzed the data from these modalities, and applied our new pipelines to external datasets. We employed scRNA-Seq of enriched non-hematopoietic cells to create a comprehensive scRNA-Seq bone marrow atlas with both hematopoietic and non-hematopoietic cells represented. We discovered nine transcriptionally distinct subtypes of human bone marrow non-hematopoietic cells and catalogued the respective cytokine contributions of each of these subtypes of cells and predicted cell-cell communication patterns. We next used CODEX to delineate the spatial relationships of the identified cell types from twelve healthy bone marrow samples. We used our novel 53 antibody panel to identify and annotate cell types in the bone marrow and then performed unsupervised neighborhood analysis to map their spatial associations. We found that myelopoiesis was spatially segregated, with the earliest HSPCs found near adipocytes, early myeloid progenitors found most predominantly in a hyperoxygenated arterio-endosteal niche, and mature myeloid elements found near sinusoids. We applied our CODEX healthy atlas to new bone marrow images from AML patient core biopsies, where we found stromal cell expansion and increased association with leukemic blasts. Collectively, this work represents significant development of methods for systematic approaches to study human bone marrow microenvironment, the first comprehensive scRNA-Seq and CODEX atlases, and, an important reference for future investigation of the human bone marrow microenvironment.