Here we report a new find of abundant woody debris and cones in stratum of two sections located to the east of the Qinghai Lake basin in China. Analysis of the anatomical structure of the wood and cones confirmed that they are Picea crassifolia Kom. The results of accelerator mass spectrometry 14C dating indicate that the buried Qinghai spruce grew during 9.7–4.2 ka, and the ages of the large trunks or branches are mainly concentrated within the interval 7.5–6.5 ka. This finding gives direct evidence at the species level about the presence of coniferous forest in the early–middle Holocene in Qinghai lake basin. In addition, the buried cones suggest that the early-middle Holocene environment was suitable for the propagation of Picea crassifolia Kom. The variations in the occurrence of Qinghai spruce forest in the Holocene probably reflect changes in humidity/moisture. The humid early-middle Holocene was suitable for the growth and reproduction of Qinghai spruce forest, while a shift toward an increasingly arid climate during the late Holocene resulted in the disappearance of Picea crassifolia Kom. from the Qinghai Lake basin, although human activities may also have contributed to the environmental change.