The application effect of isoelectric points（pI） of peptide and protein drugs containing different molecular weights and complex charge heterogeneity was evaluated by capillary isoelectric focusing electrophoresis-whole column imaging detection（cIEF-WCID ）.The pI of standard polypeptide was mensured repeatedly to verify that cIEF-WCID had a high accuracy and a good repeatability（RSD<0.50%）.Four serum protein isomers had achieved baseline separation.Gan Lai insulin was detected only a single characteristic peaks（pI 5.95±0.01） when repeating the test.The proportion differences of the characteristic peakPI were significant，when comparing the recombinant human growth hormone bulk and final，and the final appeared new characteristic peaks.Comparing the imported and domestic Avastin，manufacturer 1 and 3 were found to be consistent with the innovator drug，and the migration behavior of main component in manufacturer 1 was highly consistent with the innovator drug，however，the charge heterogeneity of manufacturer 2 was influenced because of lose K，N-term pyro-Glu.The optimized pI detecting conditions of the recombinant human follicle stimulating hormone were obtained by studying co-solvent concentration，electrolyte and focusing time,namely Co-solvent:2 mol/L urea，ampholytes at pH 2.5-5.0 and pH 3.0-10.0 mixing by 1∶1，and focus voltage:1 000 V（1 min） to 1 800 V（4 min） and to 2 200 V（1 min）.cIEF-WCID was fast and accurate，and it owned excellent resolution and reproducibility，especially，it could trace the focusing process of the analytes.Therefore，it was fit for analysing complex charge heterogeneity of protein drugs .