The invention provides physalis pubescens-green apple composite jam and a preparation method thereof. The physalis pubescens-green apple composite jam comprises the following components in parts by mass: 40-60 parts of physalis pubescens, 40-60 parts of green apple, 0.15-0.20 part of citric acid, 30-40 parts of white granulated sugar and 0.3-0.5 part of pectin, and is prepared by the steps of raw material selection, pretreatment, pickling, softening, pulping, heating and concentrating and sealing and sterilizing. In the invention, the product is ginger and glossy, has mixed fragrance of physalis pubescens and green apples as well as moderate sourness and sweetness, has the advantages of uniform body, no layering or dehydration, delicate mouthfeel and convenience in smearing, and is natural and nutritional composite jam suitable for people of all ages; and moreover, the technology is simple, the equipment is easily available, the operation is simple and convenient, and industrial production is facilitated.