Neoporphyra haitanensis is an economic seaweed widely cultivated along the coast of China, allowing 4–5 times harvests during a cultivation season. The composition and functions of algal-microbial communities are intricate, dynamic, and closely linked to the health of algae. This study utilized metagenomic and 16S ribosomal RNA (rRNA) sequencing to investigate the dynamic changes in the phycospheric microbial communities of Neoporphyra haitanensis (PMC-Nh) and bacterial communities of surrounding seawater (BC-SW) during the cultivation cycle, providing valuable reference data for monitoring and preventing diseases of cultivated seaweed. The results indicated that N. haitanensis might possess the ability to “recruit” and “select” surrounding microbial communities. Beneficial bacteria contributing to carbon, nitrogen, sulfur or phosphorus cycles, such as Proteobacteria, Firmicutes, Cyanobacteria at the class level, and Rhodobacteraceae, Saprospiraceae, Flavobacteriaceae at the family level, exhibited increased abundance. A symbiotic relationship based on resource supply formed between algae and PMC-Nh. However, potential pathogenic bacteria capable of degrading algae, such as Aquimana, Nonlabens, Alteromonas, Loktanella, also successfully colonized. The yield and quality of N. haitanensis in the 2nd and 3rd harvests are crucial for annual production and income. However, potential pathogenic bacteria and factors peaked in abundance during the 2nd harvest. At this point, the symbiotic body formed by Neoporphyra and the PMC-Nh was in a state of equilibrium on the “tip of the needle”. Biomarkers in the 2nd harvest, such as Nonlabens and Alteromonas, have been reported as algal pathogens. Moreover, pathways or factors associated with bacterial pathogenesis were significantly enriched in the algal-associated microbial community in the 2nd harvest, such as biofilm formation, flagellar assembly, bacterial secretion system pathways, and virulence factors of the Virulence Factors of Pathogenic Bacteria (VFDB) database. This may be attributed to the variable and frequently intense temperature increases in the coastal areas of the East China Sea during the 2nd harvest period in mid to late October, leading to significant shifts in microbial balance. The PMC-Nh remained relatively stable during the 3rd harvest. Until the end of cultivation, pathways related to glycometabolism and the content of glycoside hydrolases in the PMC-Nh increased, possibly due to heightened polysaccharide content and the maturation or senescence of the final stage of N. haitanensis, favoring polysaccharide exudation. Our results suggest that the 2nd harvest stage is a high-risk period for N. haitanensis cultivation, and effective cultivation management should be conducted to prevent widespread algal decay and reduce production losses.