We demonstrate through two case studies, one on thep-spin interaction model and the other on the randomK-satisfiability problem, that a heterogeneity transition occurs to the ground-stateconfiguration space of a random finite-connectivity spin glass system at a certain criticalvalue of the constraint density. At the transition point, exponentially many configurationcommunities emerge from the ground-state configuration space, making the entropy densitys(q) of configuration-pairs a non-concave function of the configuration-pair overlapq. Each configuration community is a collection of relatively similar configurations and it formsa stable thermodynamic phase in the presence of a suitable external field. We calculates(q) by the replica-symmetric and the first-step replica-symmetry-broken cavity methods, andshow by simulations that the configuration space heterogeneity leads to dynamicalheterogeneity of particle diffusion processes because of the entropic trapping effect ofconfiguration communities. This work clarifies the fine structure of the ground-stateconfiguration space of random spin glass models, it also sheds light on the glassy behaviorof hard-sphere colloidal systems at relatively high particle volume fractions.