Sub-micron elasticity of double-stranded DNA (dsDNA) governs central processes in cells such as interactions with DNA binding proteins, and therefore has been of interest for decades. Although magnetic tweezers (MT) has numerous advantages for studying DNA mechanics, the technique faced multiple challenges in probing short DNA fragments under 1 μm, hindering its application to nanoscale elastic measurements. Here, we introduce an MT-based scheme that enables precise force-extension measurements in the 100-nm regime. The method corrects for the underestimated extension resulting from magnetic bead anisotropy in a simplified, force-dependent manner. It also normalizes the variability in magnetic forces across multiple beads exploiting a DNA hairpin as a force standard. The method is simple and can easily be integrated into standard MT assays in real-time tracking. Applying this procedure, we measured the length- and sequence-dependent elasticity of short DNA down to 198 bp. The worm-like chain persistence length decreases considerably with contour length. The persistence length also steeply depends on GC content, suggesting a potential sequence-dependent mechanism for short-DNA elasticity.