Quantum optical microcombs in integrated ring resonators generate entangled photon pairs over many spectral modes, and allow the preparation of high-dimensional qudit states. Ideally, those sources should be programmable and have a high generation rate, with comb lines tightly spaced for the implementation of efficient qudit gates based on electro-optic frequency mixing. While these requirements cannot all be satisfied by a single resonator device, for which there is a trade-off between the high generation rate and tight bin spacing, a promising strategy is the use of multiple resonators, each generating photon pairs in specific frequency bins via spontaneous four-wave mixing. Based on this approach we present a programmable silicon photonics device for the generation of frequency-bin-entangled qudits, in which bin spacing, qudit dimension, and the bipartite quantum state can be reconfigured on chip. Using resonators with a radius of $22\phantom{\rule{0.2em}{0ex}}\text{\ensuremath{\mu}}\mathrm{m}$, we achieve a high brightness [about $\mathrm{MHz}/(\mathrm{mW}{)}^{2}$] per comb line with a bin spacing of 15 GHz, and fidelities above 85% with maximally entangled Bell states up to a Hilbert space dimension of 16. By individually addressing each spectral mode, we realize states that cannot be generated on chip using a single resonator. We measure the correlation matrices of maximally entangled two-qubit and two-qutrit states on a set of mutually unbiased bases, finding fidelities exceeding 98%, and indicating that the source can find application in high-dimensional secure communication protocols.