A pilot-scale study on start-up and stable operation of mainstream partial nitrification-anammox biofilter (PN/AF) system was conducted. The partial nitrification system was controlled based on online pH-dissolved oxygen (DO) linkage control strategy for nitrite oxidizing bacteria (NOB) out-selection. The immobilized anammox system was an upload biofilter reactor where anammox bacteria were immobilized on the volcanic carriers. The results showed that the nitrite accumulation ratio (NAR) was maintained above 90%, and the NO2-N/NH4+-N value was kept at 0.96 +/- 0.18 in the effluent of the partial nitrification system; the mean ammonia concentration of the effluent was below 5 mg/L, and total inorganic nitrogen (TIN) removal loading could achieve 0.11 kg/m(3).d after the stable operation in the whole system. The results of high-throughout sequencing showed that the NOB (mainly Nitrospira, Nitrotoga) was out of the partial nitrification system after 30-day operation, the relative abundance of which is less than 1% observed from Krona maps, and ammonia oxidizing bacteria (AOB, mainly Nitrosomonas) became the dominant species of nitrobacteria, the 8% of AOB stabilized finally. Dominant anammox bacteria was identified as genus Candidatus Brocadia, and one kind of rare anammox named Asahi BRW_2 was found to be at the downside of the volcanic biofilter reactor. It could be found the online pH-DO linkage control strategy allowed out-selection of NOB from the mainstream SBR system, and realized a stable partial nitrification. In addition, high DO (2.5 +/- 0.5 mg/L) condition was found to be favorable for NOB out-selection and the stabilization of nitritation. The anammox bacteria could be well immobilized in volcanic carriers, with an ability of low ammonia resistance. The study was helpful for engineering application of mainstream anammox process.