The latest requirement of optical imaging is to visualize vital, thick, and complex biological tissues in real-time and minimum-invasive mode. Among diverse available diagnostic tools, multi-photon imaging (MPI) with long wavelength excitation and exceptional lateral resolution has been a perfect option. However, the existing palette of MPI contrast agents either suffers from sub-optimal imaging performance or non-negligible risk in biosafety, exploration of suitable probes is thus of great significance. To address these concerns, in this work, pure organic nanocrystals (NCs) were developed based on aggregation-induced emission luminogens (AIEgens) (DPTA-BT) with an ultrasound-assisted method. Compared to the amorphous DPTA-BT nanoparticles (NPs), NCs with orderly arranged molecules exhibited highly enhanced nonlinear optical signals, including up to 15.35 folds of two-photon action cross-section (2PACS) and up to 4.11 folds of three-photon action cross-section (3PACS). The combination of MPI and DPTA-BT NCs has contributed to a 1900 μm imaging depth of vasculature after craniotomy and a 765 μm imaging depth through the intact skull. The safe use of DPTA-BT NCs was verified by the in vitro and in vivo biosafety assessment. This work is thus expected to encourage more innovation in the development of organic contrast agents for MPI.