Enstatite achondrites (including aubrites) are the only differentiated meteorites that have similar isotope compositions to the Earth-Moon system for most of the elements. However, the origin and differentiation of enstatite achondrites and their parent bodies remain poorly understood. Here, we report high-precision mass-independent and mass-dependent Cr isotope data for 10 enstatite achondrites, including eight aubrites, Itqiy and one enstatite-rich clast in Almahatta Sitta, to further constrain the origin and evolution of their parent bodies. The ε⁵⁴Cr (per 10,000 deviation of the mass bias corrected ⁵⁴Cr/⁵²Cr ratio from a terrestrial standard) systematics define three groups: main-group aubrites with ε⁵⁴Cr = 0.06 ± 0.12 (2SD, N = 7) that is similar to the enstatite chondrites and the Earth-Moon system, Shallowater aubrite with ε⁵⁴Cr = −0.12 ± 0.04 and Itqiy-type meteorites with ε⁵⁴Cr = −0.26 ± 0.03 (2SD, N = 2). This shows that there were at least three enstatite achondrite parent bodies in the Solar System. This is confirmed by their distinguished mass-dependent Cr isotope compositions (δ⁵³Cr values): 0.24 ± 0.03‰, 0.10 ± 0.03‰ and −0.03 ± 0.03‰ for main-group, Shallowater and Itqiy parent bodies, respectively. Aubrites are isotopically heavier than chondrites (δ⁵³Cr = −0.12 ± 0.04‰), which likely results from the formation of an isotopically light sulfur-rich core. We also obtained the abundance of the radiogenic ⁵³Cr (produced by the radioactive decay of ⁵³Mn, T_1/2 = 3.7 million years). The radiogenic ε⁵³Cr excesses correlate with the ⁵⁵Mn/⁵²Cr ratios for aubrites (except Shallowater and Bustee) and also the Cr stable isotope compositions (δ⁵³Cr values). We show that these correlations represent mixing lines that also hold chronological significance since they are controlled by the crystallization of sulfides and silicates, which mostly reflect the main-group aubrite parent body differentiation at 4562.5 ± 1.1 Ma (i.e., 4.8 ± 1.1 Ma after Solar System formation). Furthermore, the intercept of these lines with the ordinate axis which represent the initial ε⁵³Cr value of main-group aubrites (0.50 ± 0.16, 2σ) is much higher than the average ε⁵³Cr value of enstatite chondrites (0.15 ± 0.10, 2SD), suggesting an early sulfur-rich core formation that effectively increased the Mn/Cr ratio of the silicate fraction of the main-group aubrite parent body.