The Hanjiang Formation of Langhian age (middle Miocene) in the Pearl River Mouth Basin (PRMB), South China Sea consists of deltaic siliciclastic and neritic shelf carbonate rhythmic alternations, which form one of the potential reservoirs of the basin. To improve stratigraphic resolutions for hydrocarbon prospecting and exploration in the basin, the present study undertakes spectral analysis of high-resolution natural gamma-ray (NGR) well-logging record to determine the dominant frequency components and test whether Milankovitch orbital signals are recorded in rhythmic successions. Analytical results indicate the orbital cycles of precession (~19 ka and ~23 ka), obliquity (~41 ka), and eccentricity (~100 ka and ~405 ka), which provide the strong evidence for astronomically driven climate changes in the rhythmic alternation successions. Within biochronological constraint, a high-resolution astronomical timescale was constructed through the astronomical tuning of the NGR record to recent astronomically calculated variation of Earth’s orbit. The astronomically tuned timescale can be applied to calculate astronomical ages for the geological events and bioevents recognized throughout the period. The first downhole occurrences of foraminifers Globorotalia peripheroronda and Globigerinoides sicanus are dated at 14.546 Ma and 14.919 Ma, respectively, which are slightly different from earlier estimates in the South China Sea. When compared with the global sea-level change chart, the astronomical estimate for the sequences recognized based on microfossil distributions have the same end time but the different initiation time. This is probably due to the local or regional tectonic activities superimposed on eustatic rise which postponed the effect of global sea-level rising. Astronomical timescale also resolves the depositional evolution history for the Langhian Stage (middle Miocene) with a variation that strongly resembles that of Earth’s orbital eccentricity predicted from 13.65 Ma to 15.97 Ma. We infer that the main factor controlling the variability of the sedimentation rate in the Hanjiang Formation is related to the ~405-ka-period eccentricity.