Efficient activation of peroxymonosulfate using cobalt-based heterogeneous catalytic composites to produce highly reactive oxygen species for the degradation of toxic organic pollutants has been paid increased attention nowadays; however, the concept of transforming bio-waste into valuable cobalt-based catalysts remains much room to undertake. Herein, the natural marine bio-waste shrimp shell with a high total silicon content was firstly utilized as functional matrix for cobalt species to activate peroxymonosulfate for environmental remediation is reported. Remarkably, benefiting from the cooperative synergistic effect between in-situ formed CoSiOx and biochar, onto which is enriched in abundant surface functional groups, the resultant Co-SSP-700 with high specific surface area and outstanding stability exhibited prominent activity for ciprofloxacin degradation, namely nearly 90% of ciprofloxacin could be achieved within 40 min. EPR spectroscopy and scavenger tests were conducted out to investigate oxygen species, illustrating that the possible activation mechanism of PMS mainly ran through the multi-reaction pathways, whereas the radical mechanism induced by SO4•− and O2•− was a determining factor. More importantly, the intermediates of ciprofloxacin degradation were identified by LC-MS analyses to propose the possible degradation pathways and the aquatic toxicity of intermediates was explored by constructing a QSAR model.