To investigate the effects of temperature and salinity on filtration and oxygen consumption rate of Scapharca broughtonii spat with different growth stages. This study was conducted under six different water temperatures and five different salinity conditions. The spat were divided into three groups of different shell sizes and filtration rates were estimated by Neutral red. The results showed that in all of the three groups, the highest filtration rates appeared at 20 °C, and the highest one was 1.89±0.12 L g h−1 in the group with the lowest shell length (11.8±2.1 mm). The filtration rates in every group increased with the rise of salinity in the range from 10 to 40 g L−1, and the highest one is 2.62±0.21 L g h−1 in the lowest shell length group. The trends of oxygen consumption rates were similar to filtration rates. The highest rates were 0.189±0.003 mg g h−1 at 20 °C and 0.308±0.018 mg g h−1 at a salinity of 40 g L−1 in the group with the lowest shell length. And the results showed that the smaller the shell size, the higher the filtration and oxygen consumption rate.