The invention provides preparation of a compound enzyme rich in acidic pectinase as well as a strain and application of the compound enzyme. A cultured fermentation product contains pectinase, xylanase, mannase, acid protease, cellulase, amylase and beta-glucanase. Aspergillus niger is named as aspergillus niger BAK200345, and the preservation number of the aspergillus niger is CGMCC No.19614. Thecompound enzyme rich in acidic pectinase provided by the invention is rich in pectinase types, and pectinesterase, pectate hydrolase, pectate lyase, polygalacturonase and rhamnogalacturonase exist, so that the compound enzyme is a complete pectinase system. The enzyme activity of the acidic pectinase is relatively high and can reach 132960 U/g at most; the compound enzyme can reduce the feed-eggratio, increase the laying rate of laying hens, reduce the excrement sticking phenomenon and improve the intestinal health, and is good in application effect.