Background/Objectives: Antibiotics are routinely used in crustacean larviculture to mitigate bacterial infections, yet their widespread application compromises larval ontogeny. Probiotics and microalgae offer sustainable alternatives, but their combined molecular effects in crustacean larvae remain poorly characterized. This study aimed to evaluate the physiological and transcriptomic impacts of a probiotics–microalgae consortium versus antibiotics in mud crab (Scylla paramamosain) zoea, with the goal of elucidating mechanisms underlying improved larval development and identifying potential antibiotic alternatives. Methods: Scylla paramamosain larvae were reared under five treatments: clear water control (CN), microalgae alone (MA), probiotics alone (PB), a probiotics–microalgae consortium (PB-MA), and the antibiotic (AB) florfenicol. Samples were collected at 6 h and 24 h post-treatment during the first (Z1) and third (Z3) zoeal stages. Growth performance was assessed via survival and larval stage index, and multi-time point transcriptomic sequencing was performed to analyze dynamic gene expression profiles. Results: The PB-MA consortium significantly enhanced stage-specific survival from Z3 to Z5 and accelerated developmental progression compared to control and antibiotic groups. Transcriptomic analysis revealed from 492 to 2854 differentially expressed genes across treatments. PB-MA treatment was associated with the sustained upregulation of immune-related pathways (lysosome and Toll/Imd signaling), oxidative stress responses (peroxisome and glutathione metabolism), and energy metabolism (TCA cycle and carbon metabolism), whereas antibiotics predominantly suppressed these pathways. Key candidate genes, including NPC1, NAGA, ACOX1, HAO1, MUT, and PK, were prominently induced in PB-MA-treated larvae. Conclusions: The probiotics–microalgae consortium enhances basal immunity, antioxidant capacity, and metabolic adaptability in mud crab larvae at the molecular level. These findings provide transcriptomic evidence supporting the replacement of antibiotics with synergistic microbial consortia in sustainable crustacean larviculture.