Pycnometer method has been widely used in sediment concentration measurements such as river hydrological measurement, model test of river engineering, evaluation of water quality and water intake in industry and agriculture. However, when sediment concentration is low, the sediment concentration measured by pycnometer method is usually greater than the actual value because the content of dissolved matter is big. In face of such phenomenon, test engineers often doubt error of test instruments or test process, but can’t find the real reasons. Through the sediment concentration measurement of desilting basin test of water supply in a city, we found that the content of dissolved matter in the water is crucial to the measurement error of low sediment concentration; nevertheless, temperature greatly affects sediment concentration, and the smaller the sediment concentration is, the bigger the effect of temperature error is. On this basis, we put forward the improved pycnometer method to measure low sediment concentration, and test results by the method is basically consistent with those by drying method. Finally, it can provide reference for test with low sediment concentration.