The hard clam (Meretrix lusoria) is an economically important species of marine bivalve; however, for the past few years, tremendous economic losses in clam culture have been caused by poor aquaculture management approaches, global warming, and pathogens. Vibrio is a serious problem that restricts the culture industry. Probiotics could be used to promote growth, improve water quality, reduce environmental pathogens, and enhance the immunity of cultured species. We explored the use of Bacillus pumilus D5 and its mutants to perform these functions. Over a six-month experimental period, hard clams treated with B. pumilus D5 exhibited improved growth compared with those treated with B. pumilus NG25 and controls. The concentration levels of ammonia and hydrogen sulfide in treated hard clams significantly decreased compared with those in controls. Six months after the start of the experiments, the hard clams were challenged with Vibrio alginolyticus and Vibrio vulnificus, and significant differences in hard clam survival were observed between the probiotic treatment and control groups. The cumulative mortality of the control group was 60%, whereas the cumulative mortalities of probiotic-treated hard clams were 30% for B. pumilus D5 and 20% for B. pumilus NG25. Subsequently, real-time PCR was employed to determine the mRNA levels of C-type lectin (Mm-Lec1). In the bacteria exposure test, the expression of C-type lectin genes was upregulated in the B. pumilus NG25 and B. pumilus D5 groups compared with that in the control groups, and the mRNA expression level was highest at 72 h, C-type lectins play defensive roles against Vibrio invasion in hard clams. B. pumilus strains appear to represent ideal multifunctional probiotic bacteria, with the capacity to address mortality issues and increase aquaculture profitability.