Phenylalanyl-tRNA synthetase (PheRS), a member of aminoacyl-tRNA synthetase family, was the new target of anti-tubercular drug discovery. In an attempt to fully exploit the new potential anti-tuberculosis drugs presented in micro-organisms, we developed a high-throughput screening assay against Mycobacterium tuberculosis (Mtb) PheRS and then screened a library consisting of 32,000 strains and 1500 natural product-derived compounds. One potent hit extract of Penicillium griseofulvum CPCC-400528 was identified. In this study, isopatulin (1), (+)-epiepoformin (2) and gentisyl alcohol (3), three patulin-producing intermediates, together with three indole-tetramic acids, alpha-cyclopiazonic acid (4), beta-cyclopiazonic acid (5) and iso-alpha-cyclopiazonic acid (6), were isolated and identified as bioactive constituents from P. griseofulvum CPCC-400528. Their structures were elucidated on the basis of spectroscopic data. Compounds 1, 3, 4, and 5 exhibited Mtb PheRS-inhibiting activities, as well as moderate to weak anti-tuberculosis activities against Mtb H37Rv.