To overcome a series of challenges in tumor therapy, modular-agent probes (MAPs) comprised of various functional modules have been proposed. Researchers have tried to optimize the MAPs by exploiting the new modules or increasing the numbers of module, while neglecting the configuration of various modules. Here, we focus on the different spatial arrangements of existing modules. By utilizing a tetraphenylethylene (TPE) derivative with stereochemical structure and dual modifiable end-group sites as small molecule scaffold, two MAPs with same modular agents (module T for enhancing the internalization of MAPs by tumor cells and module M for causing mitochondrial dysfunction) but different spatial arrangements (on the one side, TM-AIE, and two sides, T-AIE-M, of the molecule scaffold) are designed. T-AIE-M with larger RGD binding angle performed higher specificity, while TM-AIE characterizing longer α-helix structure displayed superior toxicity.© 2021 Wiley-VCH GmbH.