A new method using ultrasonic extraction and solid phase extraction (SPE) clean-up pretreatments was developed for the analysis of mono-, di- and tri-substituted polyfluoroalkyl phosphates (abbreviated as mono-PAPs, di-PAPs and tri-PAPs) and perfluorinated phosphonic acids (PFPAs) in sludge from wastewater treatment plants (WWTPs). For the ultrasonic extraction of three mono-PAPs, three di-PAPs and three PFPAs in sludge samples, a mixture of tetrahydrofuran/acetic acid (1:1, v/v) was found to be the most suitable extraction solvent. The subsequently optimized clean-up and enrichment procedures were carried out with weak anion exchange (WAX) cartridges in-line coupled with graphitized carbon black (ENVI-Carb) tubes. Two tri-PAPs were ultrasonically extracted by acetonitrile/tetrahydrofuran (1:1, v/v) and cleaned by mixed-mode anion exchange (MAX) in-line coupled with ENVI-Carb cartridges. The analytes were analyzed by optimized high performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS) method either in negative or positive ionization mode. The method quantification limits (MQLs) of the 11 analytes in sludge ranged from 0.6 to 5.1 ng/g, meanwhile the total recoveries of the pretreatment varied from 24% (6:2 mono-PAP) to 107% (PFDPA). The method was successfully applied to analyze 16 sewage sludge samples collected from seven provinces in China, and two mono-PAPs were identified with concentrations ranging from <MQLs to 10.7 ng/g.