This paper presents an experimental investigation on the ultra-soft marine soil recovered from the seabed in deep-water areas in South China Sea (SCS). An improved T-bar penetrometer is made and employed in laboratory to measure the undrained shear strength of the soils and its degradation with the penetration cycles. A further investigation on the microstructure of the marine soils during the cyclic penetration has been conducted. The findings indicate that there is a kind of “crust zone” existing in the upper layer of seabed sediment. The reasons of this “crust zone” are further interpreted. By comparing the intact and remoulded samples, it is found that the former exhibits a higher strength degradation degree than that of the latter. This discrepancy in shear strength degradation between the two kinds of samples can be attributed to the microstructure changes. During the cyclic penetration process, the natural flocculated structure of intact soil samples collapses with the breakage of particle aggregates, and a further destruction of large-sized inter-particle pores occurs. As far as the remoulded soil samples, their microstructures experience a continuing fracturing course starting with a dense packing of soil particles and followed by a progressive development of the loose packing state.