An apparatus comprises a processing device configured to maintain a deduplication data structure comprising sub-portions associated with different compression ratio ranges and having different numbers of data block identifiers. The processing device is also configured to identify a given data block identifier and a given compression ratio for a given data block to be stored, and to determine whether the given data block identifier is in a given one of the sub-portions having a given compression ratio range including the given compression ratio. The processing device is further configured, responsive to determining that the given data block identifier is not in the given sub-portion, to write the given data block to a physical space block of the storage system and, responsive to determining that the given data block identifier is in the given sub-portion, to increment a deduplication reference count for the given data block identifier.