Site engineering is an important modulation strategy for adjusting the physicochemical properties of lanthanide luminescent ions and shows growing applications in the optoelectronic field. Herein, we explored the influence of changing M2+ (or RE3+) ions on the occupation preference of Pr3+ ions and related crystal-field splittings in Pr3+:M3RE4O9 (M = Sr and Ba; RE = Sc, Y, Lu). The obtained results indicated that Pr3+ ions possess two kinds of doping sites (M2+ (Site Ⅰ) and RE3+ (Site Ⅱ)) in Pr3+:Ba3Lu4O9 and Pr3+:Ba3Y4O9, while only occupying Site Ⅰ in Pr3+:Sr3Sc4O9 and Pr3+:Ba3Sc4O9. The variation of RE3+ ions has little impact on the crystal-field splitting of both the two types of Pr3+ luminescent sites, and by contrast, replacing M2+ ones influences the energy-level splitting of the 3H4 multiplet of Site Ⅰ obviously. Moreover, we found that the host emission of M3RE4O9 stemming from intrinsic oxygen defects shows an apparent thermally induced fluorescence quenching phenomenon. And based on the defect and Site Ⅱ emissions, both Pr3+:Ba3Lu4O9 and Pr3+:Ba3Y4O9 exhibit excellent temperature sensing performance, yielding maximum relative sensitivity (Sr) of 8.40%·K−1 (132K) and 7.89%·K−1 (129K), respectively. This work enriches the site engineering strategy in Pr3+-based optical functional materials and broadens the relevant application in temperature sensing.