Objective To differentiate pelvic floor muscle fasciitis from interstitial cystitis (IC) to study the effective treatment. Methods From February, 2014 to February, 2016, 28 patients of pelvic floor pain, with or without lower urinary tract symptoms, were differentiated in IC and pelvic floor muscle fasciitis. The IC patients (n=11) accepted hydrodistension and bladder perfusion with sodium hyaluronate 40 mg for six months, and the pelvic floor muscle fasciitis patients (n=17) accepted deep muscle stimulation (DMS) twice a day for 30 times. They were observed with pelvic floor pain and symptoms of urinary frequency, urgency score (PUF) before and after treatment. Results For the IC patients, one terminated for urinary tract infection, nine patients improved in PUF socre after treatment (t=10.854, P< 0.001); the other one without Hunner ulcer and submucosal hemorrhage, relieved after additional DMS. For the pelvic floor muscle fasciitis patients, fourteen cases improved in PUF socre after treatment (t=19.891, P<0.001), one did not finish the course of treatment, and two cases was poorly effective. Conclusion It is needed to differentiate pelvic floor muscle fasciitis from IC, which is different in treatment.