Frequency preference and spectral tuning are two cardinal features of information processing in the auditory cortex. However, sounds should not only be processed in separate frequency bands because information needs to be integrated to be meaningful. One way to better understand the integration of acoustic information is to examine the functional connectivity across cortical depths, as neurons are already connected differently across laminar layers. Using a tailored receiver array and surface-based cortical depth analysis, we revealed the frequency–preference as well as tuning–width dependent intrinsic functional connectivity (iFC) across cortical depths in the human auditory cortex using functional magnetic resonance imaging (fMRI). We demonstrated feature-dependent iFC in both core and noncore regions at all cortical depths. The selectivity of frequency–preference dependent iFC was higher at deeper depths than at intermediate and superficial depths in the core region. Both the selectivity of frequency–preference and tuning–width dependent iFC were stronger in the core than in the noncore region at deep cortical depths. Taken together, our findings provide evidence for a cortical depth-specific feature-dependent functional connectivity in the human auditory cortex.