Using Moderate Resolution Imaging Spectroradiometer (MODIS) 500 m spatial resolution global water product data, Least Squares Method (LSM) was applied to analyze changes in the area of 14 lakes in Central Asia from 2001 to 2016. Interannual changes in lake area, along with seasonal change trends and influencing factors, were studied for the months of April, July and September. The results showed that the total lakes area differed according to interannual variations and was largest in April and smallest in September, measuring −684.9 km2/a, −870.6 km2/a and −827.5 km2/a for April, July and September, respectively. The change rates for the total area of alpine lakes during the same three months were 31.1 km2/a, 29.8 km2/a and 30.6 km2/a, respectively, while for lakes situated on plains, the change rates were −716.1 km2/a, −900.5 km2/a, and −858 km2/a, respectively. Overall, plains lakes showed a declining trend and alpine lakes showed an expanding trend, the latter likely due to the warmer and wetter climate. Furthermore, there was a high correlation (r = 0.92) between area changes rate of all alpine lakes and the lakes basin supply coefficient, although there was low correlation (r = 0.43) between area changes rate of all alpine lakes area and glacier area/lake area. This indicates that lakes recharge via precipitation may be greater than lakes recharge via glacier meltwater. The shrinking of area changes for all plains lakes in the study region was attributable to climate change and human activities.