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As aerospace vehicles travel in a hellish environment, the reliability of the measuring and controlling systems has played a critical role in the credibility of a whole airborne system. Embryo-electronic system is a bionic hardware capable of self-diag- nosing and self-healing. This article presents a new approach to design embryo-electronic systems and introduces their bionic principles, system structures and fault-tolerant mechanism. As the current methods cannot meet the requirements for large-scale embryo-electronic systems, this article advances a new shift-register-based configuration memory of embryonic system to solve the problem by using the inter-cell communication to reduce the gene storage capacity of a single cell. The article designs an overall structure of the shift-register-based configuration memories of the embryonic system and connects them into a chain structure. The article also designs an inner circuit of the cell, the control of shift-register-based configuration memory and the way of runtime dynamic configuration. The simulation of field programmable gate array (FPGA) evidences the realizability of the proposed design. Compared to the SRAM-based one, this memory can save 90% of the area when constructing embryonic systems larger than 128 × 128 under the same condition.