Self-potential (SP) method has many applications, where the interpretation of SP data can be used for qualitative and quantitative interpretation. However, inversion of SP data in this paper is of quantitative interpretation and consists of highly non-linear, multimodal data and deploys global optimum method (GOM). Micro-differential evolution (MDE) is a GOM with small or micro-population size (5–8 populations) for each iteration. Consequently, this approach involves small numbers of forward computation in the inversion process. Two MDE variants, including adaptive MDE ($\mu$JADE) and vectorized random mutation factor (MVDE) were tested first for different level of noises containing synthetic SP data with single anomaly and applied to synthetic SP data of multiple anomalies. The MDE variants are reliable and effective for inverting noisy SP data. Furthermore, in order to check the rationality of MDE variants, the algorithm is applied to seven field data from different applications, including groundwater exploration, shear zone tracing, water accumulation in landslides and embankment stability assessment. The model parameters revealed by MDE variants are accurate and show good agreement with the previous results estimated using other approaches. In addition, MDE variants also require fewer forward modelling calculations than other optimization approaches.