Abstract In this work, self‐assembling tripeptides as reducing soft templates to synthesize gold nanoclusters (AuNCs) is reported for the first time. Three tripeptides (i. e., CFF, FCC, and PCF) are self‐assembled to form soft templates with different morphologies (nanofibers, nanorings and nanoparticles, respectively) by cryogenic treatment under a mixed solvent condition (tetrahydrofuran/water=8/1). All‐atom molecular dynamics (MD) simulation is used to investigate the self‐assembling process of the tripeptides. Polydispersed AuNCs with different Au core can be obtained in presence of the soft templates and the size of AuNCs shows a dependence on the soft templates. The size of AuNCs are determined by the distribution of the −SH sites on the assembled peptides skeletons and steric hindrance of soft templates. A physical model and an equation are proposed to describe the factors determining the size of aggregate AuNCs on soft templates. Finally, fluorescent AuNCs on FCC soft template were applied to bioimaging.