Achieving nanoscale strain fields mapping in intricate van der Waals (vdW) nanostructures, like twisted flakes and nanorods, presents several challenges due to their complex geometry, small size, and sensitivity limitations. Understanding these strain fields is pivotal as they significantly influence the optoelectronic properties of vdW materials, playing a crucial role in a plethora of applications ranging from nanoelectronics to nanophotonics. Here, a novel approach for achieving a nanoscale‐resolved mapping of strain fields across entire micron‐sized vdW nanostructures using four‐dimensional (4D) scanning transmission electron microscopy (STEM) imaging equipped with an electron microscope pixel array detector (EMPAD) is presented. This technique extends the capabilities of STEM‐based strain mapping by means of the exit‐wave power cepstrum method incorporating automated peak tracking and K‐means clustering algorithms. This approach is validated on two representative vdW nanostructures: a two‐dimensional (2D) MoS2 thin twisted flakes and a one‐dimensional (1D) MoO3/MoS2 nanorod heterostructure. Beyond just vdW materials, the versatile methodology offers broader applicability for strain‐field analysis in various low‐dimensional nanostructured materials. This advances the understanding of the intricate relationship between nanoscale strain patterns and their consequent optoelectronic properties.