Graphene nanobubbles (GNBs) have attracted much attention due to the ability to generate large pseudo-magnetic fields unattainable by ordinary laboratory magnets. However, GNBs are always randomly produced by the reported protocols, therefore, their size and location are difficult to manipulate, which restricts their potential applications. Here, using the functional atomic force microscopy (AFM), we demonstrate the ability to form programmable GNBs. The precision of AFM facilitates the location definition of GNBs, and their size and shape are tuned by the stimulus bias of AFM tip. With tuning the tip voltage, the bubble contour can gradually transit from parabolic to Gaussian profile. Moreover, the unique three-fold symmetric pseudo-magnetic field pattern with monotonous regularity, which is only theoretically predicted previously, is directly observed in the GNB with an approximately parabolic profile. Our study may provide an opportunity to study high magnetic field regimes with the designed periodicity in two dimensional materials.