Early childhood marks a pivotal period in the maturation of executive function, the cognitive ability to consciously regulate actions and thoughts. Mindfulness-based interventions have shown promise in bolstering executive function in children. This study used the functional near-infrared spectroscopy technique to explore the impact of mindfulness-based training on young children. Brain imaging data were collected from 68 children (41 boys, aged 61.8 ± 10.7 months) who were randomly assigned to either an intervention group (N = 37, aged 60.03 ± 11.14 months) or a control group (N = 31, aged 59.99 ± 10.89 months). Multivariate and multiscale sample entropy analyses were used. The results showed that: (1) brain complexity was reduced in the intervention group after receiving the mindfulness-based intervention in all three executive function tasks (ps < 0.05), indicating a more efficient neural processing mechanism after the intervention; (2) difference comparisons between the intervention and control groups showed significant differences in relevant brain regions during cognitive shifting (left dorsolateral prefrontal cortex and medial prefrontal cortex) and working memory tasks (left dorsolateral prefrontal cortex), which corroborates with improved behavioral results in the intervention group (Z = -3.674, P < 0.001 for cognitive shifting; Z = 2.594, P < 0.01 for working memory). These findings improve our understanding of early brain development in young children and highlight the neural mechanisms by which mindfulness-based interventions affect executive function. Implications for early intervention to promote young children's brain development are also addressed.