In the present work, the effect of phase separation on overall isothermal crystallization kinetics of two polypropylene/ethylene-propylene random copolymer (PP/EPR) in-reactor alloys was investigated. It is found that at lower crystallization temperatures (T c ), the overall crystallization rate decreases with increasing phase separation temperature (T s ). This is attributed to the lower linear spherulitic growth rate incurred by the lower PP content in the PP-rich phase at higher T s s. In contrast, at higher T c s, quenching from a higher T s to T c promotes nucleation as a result of more dramatic concentration fluctuation, leading to a faster overall crystallization rate. The overall crystallization rate of the PP/EPR in-reactor alloy prepared by multi-stage sequential polymerization process (MSSP) is retarded by increasing phase separation time (t s ). However, prolonging phase separation time has little effect on the crystallization rate of the sample prepared by two-stage polymerization process (TSP). This result can be attributed to the different phase separation rates of these two samples. The SAXS result confirms that at higher T c , phase separation in the melt before crystallization can retard crystallization, when compared with the directly quenched samples. It is also found that the phase-separated PP/EPR in-reactor alloys exhibit a larger long period because of more amorphous phases included between the lamellar crystals.