A 17-run Box-Behnken design (BBD) with three factors was used to improve the conditions for extracting astaxanthin from shrimp waste. The astaxanthin level was determined by high performance liquid chromatography (HPLC) using a C18 column and a UV detector at 476 nm. The mean extraction yield of astaxanthin at the improved conditions (extraction time 1.4 h, extraction temperature 72.4°C, and liquid-solid ratio 27.3) was 98.7 ± 2.6 µg g−1. A solid-phase extraction (SPE)-HPLC method was developed with a new hybrid organic-inorganic hybrid monolith for further purification of astaxanthin from shrimp waste. The SPE recoveries were ranging from 81.3 ± 2.4% to 86.5 ± 3.3%, and the intra-day and inter-day relative standard deviations (RSDs) of the proposed method were less than 4.3 ± 0.5% and 4.8 ± 0.2%, respectively. BBD increased the extraction efficiency and shortened extraction times significantly. SPE-HPLC with hybrid monolith showed good selectivity and purified astaxanthin from shrimp waste.