Time-synchronous development of endometrium and embryo under adequate progesterone dominance is considered integral to the process of blastocyst implantation in the human. It now appears that hypothesis-driven and candidate-based deductive approach fails to explain this complex control process. We propose a systems biology approach to elucidate the control process underlying the physiological basis of successful interfacing between embryo and endometrium towards blastocyst implantation. Elucidation of the time course pattern of transcriptomics involved in the process of blastocyst implantation in mid-luteal phase endometrium with and without progesterone dominance, as well as, with and without viable embryo shall elaborate upon the polygenic and multifactorial nature of the process of blastocyst implantation. Accordingly, a large scale homeodynamic model of hierarchical arrangement of functional networks of regulatory genomic expressional elements at the level of endometrial receptivity shall emerge. It is anticipated that such a systems biology approach shall provide an integrated picture of the process and shall also open up novel areas of basic, strategic and translational research in the biology of blastocyst implantation.