Objective To investigate the features of thyroid cystic nodules after absorption and contraction of cystic fluid in high-frequency ultrasound and contrast-enhanced ultrasound(CEUS). Methods Thrity-five cases of thyroid organized cysts were confirmed by fine needle aspiration cytology, with preoperative high-frequency ultrasound and contrast-enhanced ultrasound. Forty cases with markedly hypoechoic nodules were all papillary thyroid carcinoma(with a maximum diameter of less than 1 cm) confirmed by fine needle aspiration or surgery. The two groups both performed with retrospective analysis of the boundary, calcification, and taller-than-wide ratio and characteristics of contrast-enhanced ultrasound. Results There were significant differences in taller than wide ratio, calcification, and internal enhancement in CEUS between the two groups of markedly hypoechoic nodules (P < 0.05). Taller-than-wide ratio less than 1, the annular or semi-annular calcification, and overall no enhancement in CEUS was features of wrinkled cystic nodules, while taller-than-wide ratio greater than 1 and low enhancement in CEUS are characteristics of malignant tumors. Conclusion The ultrasonic features of thyroid cystic nodules with cyst resorption are similar to the markedly hypoechoic malignant nodules. In the markedly hypoechoic thyroid nodules with a maximum diameter of less than 1 cm, taller-than-wide ratio, the annular or semi-annular calcification of the nodules, and features in contrast-enhanced ultrasound are used to identify the two kinds of markedly hypoechoic nodules. Ultrasouond and CEUS have great significance in differential diagnosis of shrinking thyroid cystic nodules and markedly hypoechoic papillary carcinoma.