To improve the prediction of thin reservoirs with special geophysical responses, a geostatistical inversion technique is proposed based on an in-depth analysis of the theory of geostatistical inversion. This technique is based on the Markov chain Monte Carlo algorithm, to which we added the contents of facies-constrained. The feasibility of the technique and the reliability of the prediction results are demonstrated by a prediction of the sand bodies in the braided river channel bars in the Xiazijie Oilfield in the Junggar Basin. Based on the MCMC algorithm, the results show that leveraging the lateral changes in the seismic waveforms as geologically relevant information to drive the construction of the variogram and the optimization of the statistical sampling can largely overcome the obstacle that prevents traditional geostatistical inversions from accurately delineating the sedimentary characteristics; thereby, the proposed algorithm truly achieves facies-constrained geostatistical inversion. The case study of the Xiazijie Oilfield showed the feasibility and reliability of this technology. The prediction accuracy of the FCMCMC algorithm-based geostatistical inversion is as high as 6 m for thin interbedded reservoirs, and the coincidence rate between the prediction results and the well log data is more than 85%, which confirms the reliability of the technique. The demonstrated performance of the proposed technique provides a preliminary reference for the prediction of the thin interbedded reservoirs formed in terrestrial sedimentary basins and characterized by small thicknesses and rapid lateral changes with special geophysical responses.