Lake ecosystem is one of the most important component of terrestrial ecosystem on the Earth. Lakes provide essential ecological services, such as drinking water, tourism and aesthetics to humans. However, it remains unclear that how the lake ecosystems would change under the current global change pressure. It is extremely important to understand how the lake ecosystems respond to climate change as well as human activities, which would be very helpful for predicting their future changes. In order to do this, it requires longer dataset than instrumental measurements and observation. Lake sediments contain valuable information on past changes in climate, environment, and ecosystems, which could be used to investigate the influence of climate and human activities on lake ecosystems. Sedimentary pigments have been proposed as useful proxy indicators for algae and bacterial populations. Pigments were biosynthesized by phytoplankton, photosynthetic bacteria and aquatic plants and were preserved long after the end of their life cycles, which could be used to study past changes in primary productivity,phytoplankton community. Recently, a number of pigments could be better separated by reversed-phase High Pressure Liquid Chromatography. Pigments degrade in both water column and sediments. Despite losses during deposition, such as exposure to light, oxygen and zooplankton grazing, sedimentary pigments have been shown to be well correlated with changes in phytoplankton abundance and community through time, so long as there is little change in lake regions. Sedimentary pigments could be used to study changes in phytoplankton community, climatic and other environmental changes,lake stratification and redox, UV radiation, trophic sate, acidification and food-web in lakes. Pigments are also used to investigate anthropogenic influence on lake ecosystem. In this paper, we reviewed the complexity of pigments from production to sediment burial, mathematical techniques for analysis of pigment data (using CHEMTAX software and R software with BCE package) and various decay models. We suggest that sedimentary pigments could work as valuable tools to study past changes in phytoplankton community.