Phytoplankton communities are known to be affected by environmental changes such as warming and eutrophication, but relatively much is focused on diatoms and dinoflagellates dominating in coastal seas and Prochlorococcus and Synechococcus accounting for a substantial fraction of primary production in open seas. Here we show the responses of cryptophytes, which can occur in both marine and freshwater ecosystems, to multitude of environmental conditions they experience. We collected 2726 surface photosynthetic pigment samples from over 50 cruises spanning 14 years (2002-2015) in China Seas and then combined generalized additive models (GAMs) and maximum entropy modeling (MaxEnt) to describe the partial and combined effects of ocean conditions on cryptophytes. Based on GAMs, we found that cryptophytes preferred lower temperature ranging from about 5 to 16â„?and tended to prevail at higher NOx concentration. Also, an alloxanthin concentration peak at about PAR of 39 was observed. Similar results were observed when using MaxEnt to describe the probability of occurrence of cryptophytes. Pigment biomass and occurrence probability of cryptophytes in higher latitude was higher than that in lower latitude, indicating the ecological characteristic of cryptophytes’ preference for low temperature. We predicted alloxanthin concentration and occurrence probability of cryptophytes over the century using parameters as input from Earth System Models included in the Coupled Model Intercomparison Project Phase 5 (CMIP5). Our results showed that pigment biomass of cryptophytes would decrease by 1.60 ng/L from last 20 years of 20^th century (1981-2000)to 21^st (2081-2100) under scenario of Representative Concentration Pathway 8.5 (RCP8.5) on average. Also, occurrence probability of cryptophytes will decrease by 0.03, accounting for 11% of previous probability. In addition, this downward trend was inconsistent with latitude. Pigment biomass and species existence probability of cryptophytes decreased more in the low latitudes, indicating that cryptophytes would face greater challenge in low latitudes. Since cryptophytes are a crucial composition of phytoplankton communities, this decline may influence the planktonic community dynamics and coastal ecosystem functioning.