Laser heterodyne technology has high spectral resolution characteristics, and it is commonly used for atmospheric measurements, especially in the measurement of total atmospheric transmittance and gas column density inversion. For these reasons, a heterodyne system with a narrow-linewidth 3.53 μm Distributed Feedback Interband Cascade Laser (DFB-ICL) as a local oscillator was designed to measure the absorption spectrum of water vapor and methane in the atmosphere. This system has a spectral resolution of 0.002 cm-1 and a Signal-to-Noise Ratio (SNR) of 24.9 dB, which meets the requirements for Doppler broadened line shape measurements. The absolute difference between the measured total atmospheric transmittance and the simulated total atmospheric transmittance in the 3.53 μm band is less than 0.1 because of the high capability of laser heterodyne technology for spectrum detection. Therefore, the measured and simulated transmissions have the same overall variation. When combined with the least-squares method, the system realizes the simultaneous inversion of water vapor and methane column density in the atmosphere. The average column density of the water vapor and methane in the Hefei area was 1.20 g/cm2 and 1.31 mg/cm2, respectively, during the experiments. Based on this work, we have developed methods for improving spectral resolution and the signal-to-noise ratio of a laser heterodyne system, which provides the basis for obtaining more accurate absorption lines and the acquisition of more precise gas density measurements in the atmosphere.