We developed a J-compensated QHSQC NMR method for the quantitative measurement of enantiopurity and concentration of levofloxacin in a complex drug matrix. The pulse sequence can achieve uniform signal responses by the suppression of the heteronuclear coupling modulation and alleviation of the homonuclear coupling evolution. Furthermore, we discuss the influence of relaxation on peak intensities and propose the selection conditions of reference signals to achieve accurate quantifications. The evaluation of the methodology shows that the results obtained by selected peaks are in accordance with theoretical analysis with good reliability and linearity. The enantiomeric separation and quantification of levofloxacin in creams are achieved by using a chiral solvating agent, a reference compound, and the J-compensated QHSQC pulse sequence. To our knowledge, this is the first example of QHSQC methodology to quantify enantiomers in the complex matrix.