The main problem of probiotics is the low survival of these microorganisms in food products and sensitive to harsh conditions during food processing, storage and in the gastrointestinal tract. The suitable technology for protecting probiotics to maintain the high number of probiotic cells in product and survived within the host which is microencapsulation technique. The aim of this work was to investigate the effect of prebiotic which is inulin or Jerusalem artichoke on the survival of encapsulated Lactobacillus acidophilus TISTR 1338 within alginate matrix and double-coated with chitosan after freeze-drying process and heat processing at 70?C for 60 min. Furthermore, the effects of co-encapsulated cells on growth performance, survival and disease resistance in white shrimp, Litopenaeus vannamei also determined. The results showed that the highest survival after freeze-drying process of co-encapsulated cells was 3% alginate, 3% prebiotic and double coated with 0.8% chitosan condition which the survival percentage was 84.2% in inulin treatment and 85.3% treatment. In addition, the results showed that survival of co-encapsulated cells with inulin and Jerusalem artichoke were 62.8% and 68.16%, respectively that was significantly different higher than control after heat processing. From these results, co-encapsulated cells with Jerusalem artichoke could be useful to protect probiotic cells from feed processing. Consequently, the encapsulated cells were incorporated into shrimp feed supplement and cultured white shrimp for 60 days. The result showed that shrimp fed with co-encapsulated cells with Jerusalem artichoke had higher average shrimp weight gain and survival rate than control. Moreover, shrimp fed with feed supplement diet showed the cumulative mortality lower than control after challenge test with Vibrio harveyi. The study concluded that the L. acidophilus could be protected by microencapsulation technique, it can be further developed and applied in the aquaculture feed industry to prolong the life and viability of probiotic cells.