A novel extraction method, homogenate-assisted negative pressure cavitation extraction (HNPCE), was designed for the extraction and determination of the main phenolic compounds of Pyrola incarnata Fisch. by LC-MS/MS. The particle sizes and extraction yields in the process of homogenization were compared with conventional pulverization. The results showed that homogenization for less than 120 s could produce more suitable particle size powders for analyte extraction. The following NPCE parameters were optimized by a BBD test and under the optimal conditions, the maximum extraction yields of arbutin, epicatechin, hyperin, 2′-O-galloylhyperin and chimaphilin increased by 68.7%, 72.0%, 43.3%, 62.5% and 34.5% with respect to normal NPCE. The LC-MS/MS method was successfully applied for the quantification of five target compounds in pyrola, and the results of the precision test indicated a high accuracy of the present method for the quantification of the target compounds in pyrola. Furthermore, the antioxidant activities of the pyrola extracts were also determined. The results showed that pyrola had good antioxidant activities and it was a valuable antioxidant natural source.