Bottom temperature variation (BTV) is a serious problem in determining the thermal gra- dient and heat flow of the sediments in shallow seas. The water depth of the East China Sea shelf is mostly below 150m, and the heat flow measurement is strongly affected by BTV. Following a statistical algorithm, we rechecked the temperature and thermal conductivity data of the cruises KX90-1 and KX91-1, carried out by a cooperation program of China and Japan, and calculate the heat flow in a site without long-term temperature record. The calculated heat flow in the site was 58.6±3.6 mW/m2, being just within the range of the drill heat flow value of East China Sea shelf. The inversed amplitude spectrum of BTV has a peak in frequency of 1/10 per year, and the annual component is also an important part. Comparison with two lakes of Lake Greifensee and Lac Leman (i.e. Lake Geneva), which are in different water depth, revealed that with increasing water depth, the peak of amplitude spectrum moved towards low frequency components. The heat flow values calculated in this paper and from petroleum bore hole in East China Sea shelf are much more close to that in southeast China than in Okinawa Trough. Bottom temperature variation (BTV) is a serious problem in determining the thermal gradient and heat flow of the sediments in shallow seas. The water depth of the East China Sea shelf is mostly below 150m, and the heat flow measurement is strongly affected by BTV. Following a statistical algorithm, we rechecked the temperature and thermal conductivity data of the cruises KX90-1 and KX91-1, carried out by a cooperation program of China and Japan, and calculate the heat flow at a site without long-term temperature record. The calculated heat flow in the site was 58.6 ± 3.6 mW / m2, being just within the range of the drill heat flow value of East China Sea shelf. The inversed amplitude spectrum of BTV has a peak in frequency of 1/10 per Comparison with two lakes of Lake Greifensee and Lac Leman (ie Lake Geneva), which are in different water depth, revealed that with increasing water depth, the peak of amplitude spectrum moved towa rds low frequency components. The heat flow values ​​calculated in this paper and from petroleum bore hole in East China Sea shelf are much more close to that in southeast China than in Okinawa Trough.