Extracorporeal shockwave therapy (ESWT) is the primary treatment for calcific tendinitis of the shoulders, but what are the effects of clinical, sonographic, and molecular markers following ESWT in treating calcific tendinitis of the shoulder? Twenty-eight patients were categorized into radiodense and radiolucent subgroups. In addition, clinical assessments included the visual analogue scale (VAS), Constant-Murley (CM) score, American Shoulder and Elbow Surgeon (ASES) score, sonographic evaluation, and serum enzyme-linked immunosorbent assay (ELISA). The participants completed a one-year follow-up. All data were collected before and after treatment. After one year of follow-up, all patients showed notable improvement in VAS, CM, and ASES scores, with no significant clinical variations among the subgroups. However, the radiolucent group showed significant complete resorption and size reduction at the final follow-up. Sonographic evaluation revealed improved tissue perfusion and reduced calcification from 3 to 12 months in all patients, including those in the radiolucent group, but complete resorption of calcific deposits did not occur. The percentage of tissue perfusion was improved at 1 and 3 months after ESWT. There were no significant differences in the levels of the molecular markers interleukin-1 beta (IL-1 β) or IL-33, but the level of insulin-like growth factor 1 (IGF-1) was notably increased at 1 and 3 months post-ESWT. The BMP7 level was increased at 3 months and was then decreased significantly at 6 and 12 months. ESWT improved symptoms, reduced calcification, enhanced tissue perfusion, and promoted angiogenesis and BMP7 activity. In particular, it benefited radiolucent type patients with better calcification resorption. Partial resorption led to improvements in transparency, and a second ESWT session at 3 months was recommended for optimal results.