Single-molecule localization microscopy (SMLM) has pushed the resolution to sub-40 nm. Combined with structured illumination, the lateral resolution can be doubled or the axial can be improved by four-fold. However, current techniques are challenging in balancing the lateral and axial resolutions. Here we report a new modulated illumination single-molecule localization modality, isoFLUX. Utilizing two objective lenses to form interference patterns along x-z and y-z directions, the lateral and axial resolution can be improved simultaneously. Compared to SMLM, isoFLUX maintains 2-fold average enhancement in both lateral and axial under astigmatic PSF and 1.5-fold in lateral, 2.5-fold in axial under saddle-point PSF.