Thermal perception is crucial for the fitness of marine invertebrates in intertidal and shallow waters. TRPA1 is a non-selective cation channel that belongs to the TRP family with pivotal roles in initiating signal transduction of thermal perception. We investigated expression patterns of SiTRPA1 in different tissues (tube feet, coelomocytes, gonads and gut) of the sea urchin Strongylocentrotus intermedius. SiTRPA1 expression patterns under acute and long-term temperature stimuli were investigated in tube feet of sea urchins. In the present study, the highest expression of SiTRPA1 was detected in tube feet of S. intermedius. The SiTRPA1 expression level in tube feet were significantly 235.7-fold, 450.0-fold and 3299.7-fold higher than those in the coelomocytes, gonads and gut (df = 3, F = 47.382, P < 0.001). Expression levels of SiTRPA1 in the other tissues (coelomocytes, gonads and gut) were not significantly different (df = 3, F = 47.382, P = 0.972). There was no significant difference of SiTRPA1 expression among all groups in the acute temperature increase experiment (df = 4, F = 0.25, P = 0.902). In the acute temperature decrease experiment, the expression of SiTRPA1 showed no significant difference among all groups (df = 4, F = 1.802, P = 0.205). With long-term exposure (6 weeks) to different temperatures, SiTRPA1 expression in the low temperature group (10°C) was significantly higher than those in the high temperature (20°C) and the control groups (15°C) (df = 2, F = 9.57, P = 0.014). There was no significant difference of SiTRPA1 expression between the high temperature (20°C) and the control temperature (15°C) groups (df = 2, F = 9.57, P = 0.808). These results indicate that SiTRPA1 expression significantly responds to long-term low temperature but not to acute temperature decrease. The present study provides new insights on the distribution and temporal expression of TRPA1 in marine invertebrates after acute and long-term temperature stimuli.