The PubChem Substance database contains substance information (often including the chemical structure) that was submitted to NCBI by individual submitters (depositors).
The PubChem Compound records comprise a non-redundant set of standardized and validated chemical structures. A PubChem Compound record may link to more than one PubChem Substance record if different depositors supplied the same structure. Chemical names shown in PubChem Compound records are a composite derived from all linked substances, with default ranking of names by weighted frequency of use.
It is generally more useful to search for chemical names or structures in the PubChem Compound database. The PubChem Structure Search service operates on the PubChem Compound database exclusively. Search PubChem Substance if you are looking for information from a particular depositor or if you are looking for information on substances such as natural product extracts which may not have associated chemical structure information.