Seed heteromorphism (SH) is an adaptive strategy towards adversity in many halophytes. However, the underlying mechanisms and ecological significance of SH have not been deeply explored. Using Suaeda aralocaspica, a typical C4 annual halophyte without Kranz anatomy, we studied seed morphology, differentiation of morphs and fruit-setting patterns, and correlated these traits with germination responses, seed characteristics and heteromorphic seed ratio. To elucidate the genetic basis of SH, we analyzed correlated patterns of gene-expression for seed development related genes as well. We observed that S. aralocaspica produced three types of seed morph: brown, large black and small black with differences in color, size, mass and germination behavior; the latter two were further distinguished by their origin in female or bisexual flowers respectively. Further analysis revealed that SH was associated with genetic aspects including seed positioning, seed coat differentiation and seed developmental gene expression, while variations in SH may be associated with environmental conditions, e.g. annual precipitation, temperature, daylight, and their monthly distribution in different calendar years. SH and its variations in S. aralocaspica show multi-level regulation of the bet-hedging strategy that influences phenotypic plasticity, which is a consequence of internal genetic and external environmental factor interaction. Our findings contribute to the understanding of SH as a potential adaptive trait of desert plant species.