Biomolecule-directed self-assembly of -conjugated oligomers has attracted great attention in the past decade. In this contribution, two conjugates composed of quaterthiophene and tetrapeptide (Gly-Val-Gly-Val) were synthesised, namely peptide-thiophene-peptide (PTP) and thiophene-peptide-thiophene (TPT), to investigate the influence of peptide content ratio and its location in the molecular structures on the nanostructures and properties of the assemblies. Both conjugates formed organogels consisting of left-handed twisted nanostructures; however, anti-parallel -sheets were observed in PTP while parallel -sheets were obtained for TPT, although in both cases oligothiophenes adopted an H-like stacking mode. Obvious solvent-induced supramolecular chirality inversion from the oligothiophene segment was observed for PTP while such phenomenon was not clear for TPT. PTP and TPT gels also showed different stabilities towards temperature increase, as evidenced by variable-temperature circular dichroism study. From the data, it is suggested that the rational design of the location and ratio of peptide plays a key role in constructing materials with determined properties based on peptide-thiophene conjugates. Two peptide-quaterthiophene conjugates with different peptide content and location were designed, and the assemblies of the two conjugates show different packing modes and properties due to the structural difference.