Red Monascus pigments, a series of natural azaphilone alkaloids, have been utilized in China as a traditional food colorant for over 1000 years. However, instability under an acidic condition is its drawback. A new strain of Talaromyces amestolkiae was isolated in the present work, which produced the azaphilone talaromycorubrin and the corresponding azaphilone alkaloid (N-MSG-talaromycorubramine) exhibiting good stability even at pH below 3. The azaphilone alkaloid with acidic stability, an alternative of Chinese traditional red Monascus pigments, is potential for application as natural food colorant in acidic foods. The acidic stability of azaphilone alkaloid also benefits for direct fermentation of N-MSG-talaromycorubramine under a low pH condition. More importantly, correlation relationship between the terminal carboxylation of branched carbon chain of azaphilone and the stability of azaphilone alkaloids under an acidic condition is set up for the first time, which makes designing other acidic stable azaphilone alkaloids via genetic engineering become possible.