
The world No 3 beat Jun Hao 21-11, 21-19 in a match lasting 38 minutes.
World No 24 Jun Hao had no answer to the powerful smashes and tricky placements by Jonatan, who was in complete control.
Lee Zii Jia is now the only remaining Malaysian contender in the men’s singles. He will be facing Hong Kong’s Angus Ng in the opening round later tonight.
In the mixed doubles, world No 13 pair Hoo Pang Ron-Cheng Su Yin failed to clear their first round, losing to the new South Korean combination of Ki Dong Ju-Jeong Na Eun 17-21, 18-21 in 36 minutes.
Earlier, Malaysian mixed-doubles pair Goh Soon Huat-Shevon Jemie Lai cleared their first hurdle after beating Thai pair Dechapol Puavaranukroh and Suppisarah Paewsampran 22-20, 9-21, 21-18.
The All England is a BWF Super 1000 event offering a total prize money of US$1.5 million (RM6.6 million).