Multiple geochemical proxies (e.g., trace elements, δ18O and δ13C) and precise 230Th ages in speleothems are crucial for conducting robust paleoclimatic reconstructions, but the impact of diagenesis on these proxies and 230Th ages is not well-established. In this study, we investigate the petrography and geochemical composition of six aragonite-calcite stalagmites from Shennong Cave in southeastern China to analyze the transformation from aragonite to calcite (primary versus secondary) and its effects on geochemical proxies and 230Th ages. No aragonite relics are observed in columnar calcite in four aragonite-calcite stalagmites (SN55, SN49, SN104 and SNB1), although traces of aragonite exist between the calcite crystals or grow parallel at the aragonite-calcite borders. This is different from the obvious aragonite relics preserved in secondary mosaic calcite in the other two aragonite-calcite stalagmites (SN3 and SN15). Both mosaic and columnar calcite show various changes in geochemical proxies and 230Th ages compared with primary aragonite. The trend in the geochemical proxies analyzed (trace elements, δ18O and δ13C) of columnar calcite remains consistent with those of aragonite, despite significant differences in their absolute values within the overlapping periods. These differences are due to the different fractionation coefficients of isotopes and trace elements in aragonite and calcite formed under the same solution conditions rather than late diagenesis. The 230Th ages of columnar calcite are similar to those of primary aragonite, and the values of subsamples from the same calcite layer are consistent. In contrast, the trace elements and δ13C values of mosaic calcite are similar to those of primary aragonite, while its 230Th age significantly differs from that of primary aragonite, exhibiting no consistent patterns. Therefore, these geochemical characteristics of columnar calcite are significantly different from secondary mosaic calcite, indicating that the columnar calcite in these four aragonite-calcite stalagmites is primary. A comparison of trace elements and δ13C records between aragonite-calcite and pure aragonite stalagmites during the overlapping period further confirms that these columnar calcites are primary. Their geochemical proxies can be used for paleoclimate reconstruction after careful evaluation, and the transformation from aragonite to columnar calcite is caused by increased precipitation. However, due to age and geochemical proxies change, secondary mosaic calcite is unsuitable for paleoclimate reconstruction, unlike columnar calcite. This study provides competent evidence to identify whether calcite in aragonite-calcite stalagmites is primary versus secondary and whether it can be used for paleoclimatic reconstruction.