Diverse types of synapses transmit the vast information encoded in the nervous system. Even neurons of the same type can exhibit synaptic heterogeneity that alters circuit output. For instance, in the auditory system, each inner hair cell (IHC) signals to multiple Type I spiral ganglion neurons (SGNs) via glutamatergic synapses with heterogeneous properties, thereby communicating information about the frequency, timing, and intensity of the sounds we hear. Type I SGNs fall into three molecularly distinct subtypes (Ia, Ib and Ic) that make synapses with predictable differences in the position and volume of the glutamate receptor puncta, as well as the size of the apposing pre-synaptic ribbon in the IHC. To define the intrinsic mechanisms that determine subtype-appropriate synaptic properties, we investigated Maf family transcription factors, which play known roles in synapse development. Loss of c-Maf or Mafb from SGNs led to opposing effects on synaptic morphology and auditory responses, whereas loss of both c-Maf and Mafb led to formation of dysmorphic synapses and abnormal auditory responses. Further, although c-Maf and Mafb are both expressed in all SGNs, their levels differ across SGN subtypes. Single-cell RNA sequencing of single mutant SGNs revealed that c-Maf and Mafb have both shared and unique effects on subtype-specific programs of gene expression, including molecules associated with synaptic function and neuronal excitability. Double mutant SGNs, on the other hand, failed to diversify and showed dramatic changes in gene expression that included genes not changed in either single mutant. Together, these findings suggest that a combinatorial code of c-Maf and Mafb acts across SGN subtypes to establish synaptic heterogeneity that is critical for normal hearing function.