Size control of supported Pd-based intermetallic nanoparticles (i-NPs) remains a major challenge because the required high-temperature annealing for atomic diffusion and ordering easily causes metal sintering. Here, we described a pentacoordinate Al3+ site (Al3+penta) anchoring approach for the preparation of Pd-based i-NPs with controlled size, which takes advantage of the strong chemical interaction between Al3+penta sites and Pd-based i-NPs to realize size control. We synthesized six types of Pd-based i-NPs, and four of them can remain an average particle size of <6 nm. Furthermore, one of our prepared Pd-based i-NPs (that is, Pd3Pb) demonstrated outstanding performance in catalyzing the semihydrogenation of phenylacetylene.