Recently, intensive processing of marine resources has attracted considerable attention. In order to further utilize the byproducts of aquatic shellfish (Pinctada martensii meat) with high value, this study proposes a method of extracting zinc and taurine from P. martensii meat. Zinc was first extracted from P. martensii meat with an ultrasonic crusher, and then taurine was further extracted by ultrasonic-assisted water extraction from the remaining shellfish. After optimization, the biological zinc extraction rate reached 8.63%, and the taurine extraction rate reached 0.71%. Meanwhile, the parameters for cation exchange separation and taurine purification were optimized, in which the injection volume, pH value, and elution rate were set to 8.0 mL, 4.5, and 3.0 mL/min, respectively. Ultimately, the purity the extracted taurine reached 98.16%. This study provides a novel method for the extraction of biological zinc and taurine by deep processing of shellfish meat.