Aim: To prolong the shelf life of Bacillus megaterium NCT-2 by preparing microcapsules through spray drying, and evaluate their efficiency in secondary salinisation soil remediation. Methods: The wall material and spray drying conditions were optimised. Morphological characteristics of microcapsule were measured, and soil remediation effects were tested under field conditions. Results: A relatively higher survival rate of B. megaterium microcapsule was obtained with 1:1 of chitosan/maltodextrin (w/w) when spray drying was performed at 150.0 degrees C, with the feed flow rates of 800 mL h(-1) and 1000 mL h(-1), respectively. The span value of 0.93 +/- 0.01 was obtained under above conditions. Microcapsule survival rate was 64.09 +/- 0.12% after 6 months of storage. Moreover, microcapsule successfully decreased NO3- and EC value in strongly saline soil by 46.5 +/- 1.48% and 45.2 +/- 1.51%, respectively. Conclusion: Bacillus megaterium NCT-2 microcapsules have application potential in the remediation of secondary salinisation soil.