A 102-m-long ice core retrieved from the Malan Ice Cap on the Tibetan Plateau provides us with a historical record of the microorganisms trapped in the ice. The microorganisms in the Malan ice core are identified as α, ¿, and γ-Proteobacteia, and the LGC, HGC, and CFB group by means of the results of 16S rRNA sequence analysis and physiological characteristics, while the eukaryotes in the ice core are mainly composed of Chlamydomonas sp. and Pseudochlorella sp. based on the phylogenetic examination of the 18S rRNA gene. The microbial populations show observable differences at different depths in the ice core, reflecting the effects of climatic and environmental changes on the distribution of the microorganisms in the glacier. Examination of the Malan ice core shows four general periods of microbial concentration, which correspond to four phases of temperature revealed by δ18O values in the core. Observations also indicate that microorganism concentrations tend to be negatively correlated with the temperature at a relatively long timescale and, to some extent, positively correlated with mineral concentrations. The present study demonstrates that more microorganisms are associated with colder periods while fewer microorganisms are associated with warm periods, which provides us with a new proxy for the reconstruction of past climatic and environmental changes by means of ice core analysis.