The origin of ultra-compact dwarf galaxies (UCDs) is not yet clear. One possible formation path ofUCDs is the threshing of a nucleated elliptical dwarf galaxy (dE, N); however, it remains unclear how such massive nuclear stellar systems were formed in dwarf galaxies. To better establish the early history of UCDs, we investigate the formation of UCD progenitor clusters from supergiant molecular clouds (SGMCs), using hydrodynamical simulations. In this study we focus on SGMCs with masses 107-108 M⊙ that can form massive star clusters that display physical properties similar to UCDs. We find that the clusters have extended star formation histories with two phases, producing multiple distinct stellar populations, and that the star formation rate is dependent on the feedback effects of SNe and asymptotic giant branch stars. The later generations of stars formed in these clusters are more compact, leading to a clearly nested structure, and these stars will be more He-rich than those of the first generation, leading to a slight colour gradient. The simulated clusters demonstrate scaling relations between Reffand M, and σv and M consistent with those observed in UCDs and strongly consistent with those of the original SGMC. We discuss whether SGMCs such as these can be formed through merging of self-gravitating molecular clouds in galaxies at high-z.