A silicon vertex detector of the MPD tracking system was proposed for high-efficient registration of short-lived particles produced in nucleus–nucleus collisions. In this work the pointing resolution of the various vertex detector configurations based on monolithic active pixel sensors has been evaluated. It is shown that the five-layer model of the vertex detector surrounding a 40 mm diameter beam pipe has the best spatial resolution. This allows to reconstruct the decay vertices of short-lived charmed particles. The yield of D mesons, as well as the production of pions and protons, with momenta outside the region kinematically allowed for p+p interactions at central rapidities in Au+Au collisions at NICA collider energies, was estimated in the context of the application of this vertex detector.