Regulating the electronic structures and carrier dynamics in 2D materials via elastic strain is a fascinating avenue for tailoring their optoelectronic properties at atomic scale. Here, the abnormal response of indirect excitons to non‐uniform elastic strain in MoS2 flakes is reported. The non‐uniform elastic strain in the MoS2 flakes is introduced by transferring them to pre‐prepared convex cross structures on a SiO2/Si substrate, where the topography and strain distribution are determined by atomic force microscopy and Raman spectroscopy, respectively. It is observed that the emission energy of the indirect excitons shows an unexpected blue‐shift followed by a red‐shift with increasing the local tensile strain, which is in sharp contrast to the linear red‐shift of the direct excitons. Density functional theory calculations reveal that the abnormal energy shift of the indirect excitons in the MoS2 flakes arises from the strain‐induced competition between two indirect bandgap transitions and the spatial exciton funnel effect in the non‐uniform strain field. This work provides new insights into the elastic strain effect on the indirect excitons in 2D semiconductors, which possesses potential applications in flexible optoelectronic devices.