In this paper, the influence of decreasing Zr content (0.0110wt%, 0.0044wt%) on the microstructure, MnS inclusion characteristics, and mechanical properties of medium carbon ferrite-pearlite steel was studied. The results show that the volume fraction of intragranular ferrite (IGF) in steel increases with a reduction in Zr content. The ductility of the steel is reduced by 1.83%, the impact toughness is increased by 2.5 times, and the yield strength is almost unchanged. Compound MnS inclusions are the main inclusions that induce IGF formation. The proportion of heterogeneous nucleation of MnS inclusions using oxides as nucleation sites is increased, which is the main reason for the increase in the volume fraction of IGF. Furthermore, MnS inclusions change from type Ⅲ to type Ⅰ and Ⅱ, and their distribution is gradually uniform. Thermodynamic analysis reveals that the underlying cause for the morphological transformation of MnS inclusions is the rapid surge in the supersaturation of S element in molten steel. The presence of liquid-phase low-melting inclusions (MnS-Al2O3) promotes the formation of type Ⅰ MnS inclusions. The volume fraction and the dimension perpendicular to the fracture surface of the MnS inclusions are increased by at least 33% and 111%, while their aspect ratio is reduced by a maximum of up to 19%. The change in the volume fraction of MnS inclusions is the primary factor contributing to the decrease of tensile plasticity. The toughness of steel is mainly affected by the aspect ratio and the dimension perpendicular to the fracture surface of MnS inclusions.