Prospective memory (PM) refers to the ability to remember to do something in the future. Implementation intention refers to a self-regulatory strategy in the form of “If …, then …” planning that can improve PM performance. However, the neural basis of the effect of implementation intention on PM remains unclear, as do the phases of PM that are affected by implementation intention. This study aimed to address these issues. Healthy participants were randomly assigned to the implementation intention (n = 18) and typical instruction (n = 20) conditions. All of them underwent functional magnetic resonance imaging (fMRI) scanning when performing a PM task, which differentiated encoding, maintenance, and execution phases. Results demonstrated that participants in the implementation intention group showed different brain activations compared to participants in the typical instruction group. During the encoding phase, the implementation intention group showed increased activations in the inferior frontal gyrus (BA 10) and supramarginal gyrus (BA 40) compared to the typical instruction group; during the maintenance phase, the typical instruction group showed stronger activations in the inferior frontal gyrus (BA 46) than the implementation intention group; during the execution phase, the typical instruction group showed increased activations in the precentral gyrus (BA 6) and middle frontal gyrus (BA 8) than the implementation intention group. These results demonstrated the neural correlates of implementation intention on PM in different phases, and support the conclusion of our previous review based on fMRI evidence that implementation intention's improvement of PM performance is not fully automatic.