To enhance the economics of biorefinery of lignocellulosic biomass, lignin has been extensively studied as a promising feedstock for biofuels and bioproducts. This study aimed at a new lignin biotransformation platform with a strain of marine protist, Thraustochytrium striatum, by which lignin can be upgraded into high-value nutraceuticals/pharmaceuticals. It was found that this strain was able to utilize various types of lignin compounds into polyunsaturated long-chain fatty acids (EPA and DHA) and carotenoids (e.g., β-carotene and astaxanthin). In screening of 14 lignin model compounds as carbon sources, T. striatum can grow in most compounds at different concentrations, while achieving the best growth in 3, 4-dihydroxybenzoic acid (3, 4-DHBA) and 4-hydroxybenzoic acid (4-HBA). The maximum biomass yield reached 2-3 g/L under 5 g/L of 3, 4-DHBA or 2 g/L of 4-HBA even without optimization. In both batch and fed-batch cultivation modes, T. striatum can accumulate decent amount of long-chain fatty acids (25-30% cell dry weight) and carotenoids (5-10 mg/g biomass) associated with proteins and carbohydrates. T. striatum was also proven to utilize polymeric lignin. Significant cell mass growth was observed with Kraft pine lignin as sole carbon source, as well as accumulation of fatty acids and carotenoids. The investigations on lignin degradation mechanisms with NMR, GC-MS and GPC indicated that T. striatum utilized 4-HBA as a central intermediate. The monomer released from lignin depolymerization was firstly converted into 4-HBA and then catabolized by cells. The capability of T. striatum to digest a wide range of lignin materials makes it a novel and attractive platform for lignin utilization.