The dynamic changes of secondary metabolites and tyrosinase activity of Malus pumila flowers were investigated during blooming for full use of M. pumila flowers. Phlorizin, astragalin and afzelin were selected as the indicators to determine the optimum extraction conditions of M. pumila flowers by HPLC analysis and three-factor and three-level orthogonal design experiments. When the smashing mesh number was 40 mesh, the ultrasonic time was 30 min, the solid–liquid ratio was 1:120, and the centrifugal speed was 10,000 r/min, the total content of the three compounds was the highest. The total content of phlorizin, astragalin and afzelin increased firstly and then decreased, and the highest was on the third day (176.74 mg/g). At the same time, the tyrosinase activity of M. pumila flowers showed that it had an activation effect on tyrosinase during early blooming period, however it exhibited inhibitory effect during late blooming period. Electronic supplementary material The online version of this article (10.1186/s13065-019-0602-y) contains supplementary material, which is available to authorized users.