Pearl oyster (Pinctada fucata martensii) is the main species cultured for marine pearls in the world. A breeding program was carried out for desirable production traits, including high growth rate, and a fast-growing selective strain of pearl oysters was established. In the current study, we compared the growth characteristics between a selective strain and a cultured population of P. f. martensii in Beihai, Guangxi Province, China. Large size (SL) and small size (SS) individuals of the selective strain were selected, and the differences of physiological and metabolic indexes, such as feeding, respiration, excretion, and enzyme activities between SL and SS and cultured population (CL), were also compared. The results showed that at the age of 6 months, pearl oysters of the selective strain were 14.61% larger than CL, and the proportion of SL (30–40 mm) was 59%, which was two times higher than CL (28%). SL with a rapid growth rate had a high clearance rate (CR), and the CR of SL was about 1.8 times higher than that of CL and 5 times higher than that of SS. In addition, the activities of digestive enzymes (amylase, pepsin, and lipase) and growth-related carbonic anhydrase enzymes in SL were higher than those in the other two groups (p < 0.05). SS with a slow growth rate had higher oxygen consumption (OCR) and ammonia excretion (AER) rates than SL and CL (p < 0.05). Our results suggest that the rapid growth of the selective strain P. f. martensii can be attributed to increased energy intake and reduced energy consumption.